This is why I have 3 batteries... really
I have one just for electronics and two for the engine.
I don't think they will all charge properly if the switch is not made to the battery you want to charge while running. Look at the amp meter when swithing. You will find the weak battery and can target that one if you like while running back home. I think it is OK to run on both if everything is functioning alright. Most alternaters are pretty powerful these days and can handle a dual or even triple set up.
Mine was a nightmare hookup with 3 Perko switches... I had to take it apart to figure out the logic but I ripped it down and it is much simpler now with just one switch.
Hybrid Mode
