Dave, it is wired as you state. Yes, talking about the sg 200. When the ACR is connecting the house and start, it will see the capacity of both the house bank and starting. When the voltage drops, the ACR will disconnect. And the sg200 will only see the house bank. How would the sg 200 know the difference. The batt bank can keep changing sizes….
The SG 200 uses the Smart Shunt which measures current entering and leaving the house bank. The voltage is measured directly at the house battery terminal. It won't be affected by the Start Battery. You won't know the SOC for the start/reserve battery, that's not a big issue because it will seldom be discharged and when used for starting, it will be returned to 100% within minutes of starting the engine.
If the monitor measured the voltage at the alternator, you might see a difference when the ACR was open. But that would be negligible.
Let me rephrase your question a bit. What does the monitor read when there is both a load and charging source on the battery? (in your question the load would be charging the starting battery). The monitor reads how many amps are going into the battery. For example, when running my refrigeration will draw ~28 amps. When no charging source (alternator, solar, or charger) the monitor reads -28 amps. If there 10 amps of the solar is available, then the monitor reads -18 amps, because that is how much the battery is contributing to running the refrigeration. The same happens when I use battery charger (50 amp), it will supply the power to refrigerator with any extra power going to the battery if it needs it, thus the charger may be putting out the full 50 amps, the refer comes on and the monitor shows the current going into the battery dropping from 50 amps to 22 amps.
Remember an ACR only closes the circuit when a charging voltage is present, when there is no charging voltage the circuit stays open and the 2 battery banks are isolated. The charging source doesn't differentiate between a device consuming electricity and a battery needing a charge. A battery needing a charge is simply another device on the circuit that is consuming electricity.
You'll be fine with the ACR and the SmartGuage, in fact you will be better off than you are now. The two essentials are having all charge sources going to the house bank, and the shunt must be the last thing on the negative side of the circuit, i.e., only the shut is connected to the negative terminal. (Temp sensors don't count)