Basically from what I perceive here is your booster feeds a regulator, not a battery. The battery is not fed voltage to charge and your looking to get the voltage of that auxiliary battery alone while it discharges to the regulator.
If that is correct the battery is already isolated.
If your charging the auxiliary battery, in order for you to test the voltage of the battery without testing the charger at the same time, you need to have a disconnect happen during testing. Otherwise your going to only be reading the voltage of the charger and the battery (may be the same, most likely not). This can happen with transistors fairly easy or you could automate the process with op-amps or microcontrollers.
Key point being you cant test the battery under charge without getting the charger voltage mixed into it.
If your battery is additional voltage, as previously mentioned we would need to see the regulator schematic to determine if the regulator is feeding anything back into the battery or simply place a diode inline so as to not get voltage from that as feedback during testing. (should be done anyways, if not already in the regulator itself)
This looks like a UPS in my opinion and the auxiliary battery would need to be isolated from the input source if you were to charge and test simultaneously.