Hey there.
Sounds like you have a good project in front of you!
First, of course, is to physically install the battery. Next install the SmartShunt. Finally, connect the inverter, chargers, and other loads.
Dual solar charging
The idea is to have the PWM controller contribute charge during the Bulk stage, then essentially drop out during the Absorb stage. The FM80 will contribute charge during both Bulk and Absorb.
The two controllers will need to collaborate, and their common control point is battery voltage. They will need to be calibrated to agree on voltage. If that's not possible, then the difference in readings need to be accommodated in the programming.
The important parameters to adjust are the maximum charge current during Bulk, and the Absorb Voltage and Time, and Float Voltage.
Which model of the PWM controller do you have?
I couldn't find a copy of the GCSOAR manual on line, but assume one came with the controller. It will be programmed by selecting the USER mode, rather than its preset profiles (Flooded, AGM, Gel, etc.)
Step #1: Determine battery maximum charging rate.
I don't recall the battery specs, but the typical L16 6V Trojan has a 320AH capacity @ C20. Two parallel banks = 720AH. The typical AGM can handle charge rates around 20%. 720AH @ 20% = 144A, so no problem running the controllers at full output.
(Confirm these calculations.)
#2 Determine Absorb Voltage and Absorb Time
The Trojan charging specs will give the figures for Absorb charging. These values will be programmed into the FM80.
#3 Determine Float Voltage
The Trojan charging specs will give this value. It will be programmed into the FM80.
#4 Calibrate, Program and Test the FM80
Connect the FM80 to the battery (if not done already) and disconnect from the solar panels. (If physically disconnecting, rather than via a DC circuit breaker or switch, do so while the panels are NOT under load. Otherwise, a nasty DC arc may result.)
Measure the voltage at the FM80 Bat +/- terminals. Compare the measurement to the front panel Out Volt which is the FM80's internal voltmeter reading of the battery voltage. The two readings should agree. If not, the FM80 should be calibrated.
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Program the Absorb Voltage, Absorb Time, and Float Voltage into the FM80
Run it through a charge cycle and confirm its working as programmed.
#5 Connect the PWM controller to the battery.
CONNECT TO BATTERY BEFORE CONNECTING TO SOLAR PANELS. This is always important as connecting to solar panels without connecting to the battery first will damage the controller.
#6 Measure battery voltage at PWM controller terminals, and compare with front panel reading.
The battery reading at the charge controller Bat +/- terminals should agree with those at the FM80 Bat +/- terminals. Note any difference.
If the controller has a battery voltage readout, compare to the measured voltage. If the controller has a calibrate function, use it to align the measured voltage with the controller's internal voltmeter reading. Otherwise, note the discrepancy.
#7 Program the USER profile.
The Absorb stage is called "Boost", I believe.
Program the Boost voltage to be 0.1V lower than the FM80 Absorb voltage. If the controllers are both accurately calibrated, the actual parameter value will be -0.1V relative to the FM80 Absorb Voltage. If calibration is off, the Boost Voltage value will need to be adjusted accordingly. When the Absorb and Boost voltages are programmed properly, at the point the FM80 switches to Absorb, the PWM controller should go silent. (As the battery voltage will have risen above its Boost Voltage set point.)
If the PWM controller has a Boost Time setting, make it as short as possible (but not zero.)
Set the Float Voltage 0.1V below the FM80 Float Voltage.
Connect the solar panels. (It may be best to do this early in the morning before the "FM80 wakes up".)
#8 Test the two charge controllers together.
The two controllers should "wake up" and start a Bulk charge cycle.
Once the battery rises to the PWM controller's Boost Voltage, it will switch to that stage. The battery should continue to rise another 0.1V to the FM80 Absorb Voltage, and it should switch to Absorb. At about the same time, the PWM controller should go silent.
When the PWM controller drops out, the FM80 may revert to Bulk charging due to the reduction in total charge current. That's expected. The PWM will likely "wake up" and resume charging. The Absorb stage will be reached again. This cycle may repeat many times, depending on load and solar conditions. Not to worry, its just the "controller two-step" dance. Eventually enough charge will have been put into the battery so the FM80 alone can maintain Absorb.
Once Absorb is complete, the controllers will switch to Float. If the FM80 can maintain Float alone, the PWM will stay silent.
It may take a bit of voltage parameter "tweaking" on the PWM to get it operating smoothly with the FM80. The important thing is the Boost and Float voltages be a true 0 1V lower than the FM80 Absorb and Float.