The NASA instrument can only monitor one battery bank (which can include 2 or more batteries wired in parallel).
It is really intended to monitor the service battery bank, which is how I use it on Playtime. I assume, like a car battery, that the engine start battery will always be fully charged. A quick voltage check with the built in (Bavaria) voltmeter can confirm this. If the voltage is 12.6V or above, all is well.
The single shunt provided by NASA is wired into the main lead (negative, I think) to the battery bank so all current in or out of that bank flows through the shunt and is measured by the instrument.
Hope this helps