Jake has commissioned hundreds of two-stage furnaces — Goodman, Amana, Trane, Lennox, Carrier, Rheem, every brand under the sun. And no matter the brand, he keeps finding the same problem:
“Most two-stage furnaces installed in America are accidentally turned into single-stage units.”
Not because the equipment is bad.
Not because the home is wrong.
Not because the homeowner bought the wrong size.
But because:
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the thermostat isn’t compatible
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W2 isn’t wired
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dip switches are left on factory defaults
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blower speeds aren’t matched to the duct system
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the timing logic conflicts with airflow
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static pressure forces Stage 2 early
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installers never commission the system
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shortcuts collapse two-stage performance
So the system:
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never runs Stage 1
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overheats
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short cycles
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becomes loud
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blasts air unevenly
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ramps the ECM blower unnecessarily
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and frustrates the homeowner
Jake’s mission: unlock the full potential of the two-stage system — smooth, quiet, invisible comfort.
100,000 BTU 96% AFUE Upflow/Horizontal Two Stage Goodman Gas Furnace - GR9T961004CN
This article is Jake’s complete, step-by-step commissioning blueprint for a perfect two-stage install.
🧱 1. Why Most Two-Stage Systems Run Like Single-Stage Systems
Jake sees installers make the same mistakes over and over:
✔️ W2 not wired
The furnace never receives a second-stage call, so it defaults to timing logic or never uses Stage 2 at all.
✔️ Thermostat only supports single-stage
The homeowner thinks they’re getting two-stage comfort — but the stat can’t command it.
✔️ W1–W2 jumpers left in place
This locks the furnace into one-stage behavior.
✔️ Dip switches left on factory default
Which typically means:
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too much airflow in Stage 1
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too much airflow in Stage 2
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overly aggressive heating
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high noise
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uneven comfort
✔️ Blower not matched to duct capacity
High static pressure kills Stage 1.
✔️ Filter or return restricts airflow
Causes:
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high ΔT
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overheating
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forced Stage 2
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noisy operation
Jake’s rule:
“A two-stage furnace will only behave if the installer behaves.”
🎛️ 2. Thermostat Compatibility: Jake’s Staging Pass/Fail Map
A thermostat is the brain of a two-stage system.
If the brain cannot command W2, it cannot “speak” Stage 2.
Jake uses three categories:
Category A — TRUE Two-Stage Thermostats (Pass)
These have dedicated W1 + W2 terminals and true multistage logic.
Jake recommends:
✔️ Honeywell T6, T9, T10
Affordable, reliable, clean staging behavior.
✔️ Ecobee Premium & Ecobee Enhanced
Full W1/W2 support, excellent temperature averaging.
✔️ Emerson Sensi Touch
Simple interface, dependable staging.
Category B — “Pseudo Two-Stage” Thermostats (Fail)
These thermostats pretend to support staging but actually rely on timing algorithms, NOT real W2 calls.
Jake avoids:
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cheap Wi-Fi stats
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single-stage Nest models
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off-brand Amazon units
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thermostats with “adaptive intelligence” but no W2 terminal
Jake’s rule:
“If it doesn’t have a W2 terminal, it doesn’t have my respect.”
Category C — Communicating Stats (Conditional Pass)
These only work if:
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the furnace is a communicating model
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wiring and control board support it
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the entire system is matched
Jake prefers non-communicating two-stage stats for simplicity on GR9T96-style installs.
🧰 3. Wiring: The Smallest Mistakes That Kill Two-Stage Performance
Jake checks the thermostat wiring before he checks ANYTHING else.
✔️ W1 → furnace W1
Primary heat call.
✔️ W2 → furnace W2
Second-stage call — THE MOST IMPORTANT WIRE.
✔️ NO W1–W2 JUMPERS
Jake finds these constantly.
They force Stage 2 instantly.
✔️ Y1 → cooling
Ensures correct blower profiles.
✔️ G → fan
Fan-only logic must be correct.
✔️ C wire → stable power
Especially for smart stats.
Jake’s rule:
“You can’t fix staging until you fix the wiring.”
🧲 4. Dip Switches: The Secret Menu That Controls Everything
Most installers NEVER touch dip switches.
Jake touches them EVERY TIME.
On the Goodman GR9T96, dip switches control:
Heating Airflow (H1–H6)
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CFM profile
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Stage 1 vs Stage 2 airflow
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fan-off timing
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airflow ramps
Jake sets:
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Stage 1: LOW–MED
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Stage 2: MED–HIGH
He never sets Stage 1 too high because it:
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makes heat feel cool
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becomes noisy
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overdrives ductwork
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kills comfort
Cooling Airflow (C1–C6)
Only matters for matched cooling systems — but still important.
Blower Off Delay (OD1–OD4)
Controls how long the blower runs after heat shuts off.
Jake’s setting:
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90–120 seconds
This extracts remaining heat without blowing cold air.
Staging Timing & Logic Controls
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minimum runtime
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cooling interlocks
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staging delay
Jake starts with a 10–12 minute delay before Stage 2.
🌬️ 5. Blower Speed Configuration: Jake’s CFM Rules for Quiet Comfort
Jake matches blower speed to:
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duct size
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static pressure
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number of returns
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filter type
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coil resistance
He does NOT use factory-default blower settings.
✔️ Stage 1: 60–70% of max CFM
This creates:
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low noise
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smooth airflow
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consistent temperature
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long heating cycles
✔️ Stage 2: full CFM output
Used only for:
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extreme cold spells
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large temperature deltas
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quick recovery
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end-of-cycle heat distribution
Jake’s rule:
“Stage 2 is a tool — Stage 1 is a lifestyle.”
📈 6. Timing: How Long Each Stage Should Run (Jake’s Magic Numbers)
Jake uses timing to prevent the furnace from jumping to Stage 2 too fast.
✔️ Minimum Stage-1 runtime:
10–12 minutes
This prevents:
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short cycling
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noisy ramps
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hot/cold swings
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overly aggressive heating
✔️ Stage-2 eligibility only when:
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temperature hasn’t risen enough
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thermostat calls for more
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outdoor temperature is extremely low
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duct system can handle higher CFM
Jake NEVER allows Stage 2:
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during mild weather
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when static is above 0.60"
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when return ductwork is undersized
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when the home is within 1–2°F of setpoint
This is comfort engineering.
📉 7. Static Pressure & Return Design: The Triad of Staging Success
Jake’s three key staging metrics:
✔️ Return Air Volume
If returns are too small → Stage 1 becomes loud and weak.
✔️ Filter Restriction
1-inch filters → Stage 1 suffocates
4-inch filters → Stage 1 blossoms
✔️ Static Pressure
Jake’s thresholds:
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0.40–0.50" ideal
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0.60" = staging problems
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0.80" = system choking
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1.00+" = furnace in distress
If static is too high, the furnace:
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overheats
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ramps blower
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jumps to Stage 2
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short cycles
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becomes loud
Fixing static is often the key to unlocking staging.
🧊 8. Coil & Plenum Alignment: The Hidden Reason Staging Fails
Bad airflow at the coil = failed staging.
Jake checks:
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coil sits flat
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coil sits centered
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plenum height at least 18–24"
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no coil bypass
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no return turbulence
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no kinks or sharp transitions
Even perfect staging at the board is doomed if the coil is starved.
Jake’s rule:
“Staging loves low static and tall plenums.”
🔥 9. Combustion Air & Venting: The Invisible Staging Breaker
If the furnace cannot breathe, Stage 2 will:
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trigger rollout
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trip the pressure switch
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lock out the burner
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shut down
Jake checks:
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intake air path
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vent length
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elbow count
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proper slope
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no blockages
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correct PVC diameter
Staging depends on proper combustion.
🧪 10. Jake’s Complete Two-Stage Commissioning Test
Jake performs these tests in this exact order:
1. Static Pressure Measurement
Before touching anything else.
2. Filter Check
Replace 1-inch filters immediately.
3. Dip Switch Settings
Heating airflow + off-delay.
4. Wiring Verification
Ensure W1/W2 are clean.
5. Thermostat Configuration
Set correct type (2H/1C conventional).
6. CFM Verification
Check airflow tables against measured static.
7. Test Stage 1 Operation
Should be silent, smooth, stable.
8. Test Stage 2 Operation
Only after Stage 1 stabilizes.
9. Measure Temperature Rise
Must fall within furnace spec:
30–60°F for most GR9T96 units
10. Combustion Analysis
Check CO levels, vent performance, draft.
11. Duct Balance Check
Adjust supply/return balance.
12. Full Cycle Operation Test
Verify Stage 1 dominates.
Jake does not sign off on a furnace until Stage 1 feels “buttery smooth.”
🛠️ 11. Real-Home Case Study: The “Two-Stage Furnace That Wasn’t”
Home:
3,000 sq ft — two-story
Furnace: Goodman GR9T96
Thermostat: single-stage WiFi model
Symptoms:
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loud airflow
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cold upstairs bedrooms
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high-limit trips
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Stage 2 always active
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ΔT swinging between 30 and 67°F
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static = 0.82"
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noisy blower ramping
Homeowner was told:
“You bought the wrong furnace.”
Jake discovered:
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W2 not wired
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stat didn’t support staging
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dip switches on factory settings
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1-inch MERV 11 filter
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small return grille
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coil misaligned
Jake’s Fix:
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installed Honeywell T6
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wired W2 correctly
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set 12-minute Stage 2 delay
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changed blower profiles
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installed 4-inch filter cabinet
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added 12x25 return
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realigned coil
Results:
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static dropped to 0.44"
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ΔT stabilized at 40°F
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Stage 1 handled 90% of heating
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noise reduced 50%
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upstairs now even with downstairs
Jake saved the system without replacing the furnace.
🔗 12. Verified External Sources (6)
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DOE Residential Furnace Essentials
https://www.energy.gov/energysaver/furnaces-and-boilers -
ASHRAE Residential HVAC Standards
https://www.ashrae.org -
SMACNA Air Distribution Construction Standards
https://www.smacna.org
🎯 Conclusion: A Two-Stage Furnace Is Only as Good as Its Setup
Jake ends every commissioning with this:
“Two-stage comfort doesn’t come from the furnace — it comes from the installer.”
A perfect two-stage setup gives homeowners:
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whisper-quiet airflow
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reduced energy bills
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even temperatures room-to-room
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long Stage-1 cycles
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smooth, gentle heat
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long furnace lifespan
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stable temperature rise
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happier ECM blower
This is the real blueprint for two-stage mastery — Jake’s complete method, from wiring to CFM to final commissioning.
