You need first to understand how the wiring of the batteries and the switch was made.
The fact is you know to start your engine, know how to sail your boat, and you do not understand how your battery switch works.
Same happened to me.
If I were to ask a crew mate to switch one, two or both batteries, he would probably need to read a manual to understand what he was doing. This is the main reason why I swiched from a 1,2,both switch, to two tiny and ridiculous non good looking on-off switches. I get another on-off switch to paralel both banks.
I do also have alternator supplying current directly to the bank, bypassing the on-off switch.