Hey Lew,
Sonar units draw very little power. Your big engine should keep your cranking battery well - charged. I have only run mine flat once and that was due to running the livewell for 7 hours without firing up the main engine.
A pair of booster cables will let you boost from your deep cycles to the cranking battery in a pinch.
Not sure about charging both deep-cycle & cranking batteries at the same time with the same charger?The cranker is designed to recharge via alternator while the deep-cycle require a trickle charge.
I think all you'll need is a 2 bank unless running a 36V system.
>Bill