RE: Need a few electrical/genset questions answered quickly!
It sounds like if you go to "all" when the engine is running, you'll charge both batteries from the alternator. I agree that you need a combiner to prevent the two banks from draining on the hook if you forget to deselect the "all" setting.
A way to confirm this is to look at the battery voltages when the engine is running. Either use an on board voltmeter or carry a digital voltmeter on board to troubleshoot.
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