If I remember correctly the 2nd battery is just a voltage monitor, not an amp hour counter.
Think of it this way. You have a single shunt in the negative lead to both batteries. You have the switch on all (on the positive leads) the current
will flow equally to both batteries (making a lot of assumptions). Now let's say you then switch to the 1 position. You discharge to 50% then switch to the 2 position, and discharge to 80%. The meter will have seen 70% discharge, but not know really from where. Now you start the engine
while still on 2, and motor
for a length of time. 2 may be fully charged, but the meter will still show a state of discharge because the current
that came out of 1 has nothing to do with 2.