Are both battery's the same?? I mean exact!! If you have a deep cyc and a regular, or size 2 and a size 6 (just example) the bigger battery could suck down the smaller battery or the other way around.
When you go home do you leave the switch on? If so this will also cause the more needy battery to take from the better battery.
I have start battery by its self, all eletr on the 2nd battery.ride out or in it is set for all to charge them, when fishing for long times with the motor off I switch to one so the other stays good for starting.
about once a month I hit it with the charger and I have had no problems, even when using the live well all day.
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1986 V20 
Old Fishermen never die, we just SMELL that way!!
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