Re: On board charger question
Normally, an on board charger has isolated battery chargers, so each one is hooked up to a separate battery and charges it independently of the others no matter how it's hooked up.
One caveat. If you have unmatched batteries in your trolling system, and a "run or charge" switch on said system, when the switch is in "charge" or maybe "12", the batteries are wired in parallel. One battery may prevent the other from taking a charge because of unmatched characteristics. Characteristics of a battery change considerably as they age.
So, make sure the "run-charge" switch is in the run position, and measure the voltage across each battery as it's charging. If there's a dead bank on the charger it'll show up as low voltage.
hope it helps
John