Positive to positive, negative to negative for 12V hookup...hook up your trolling motor to one of the batteries just as you would if it were one battery...pos to pos, neg to neg. I would however consider hooking my electronics up to the cranking battery....if you hook them up to the same battery as your trolling motor you may get interference from the trolling motor. Electronics have a very small power drain...just make sure you switch off your main power switch after your done for the day or turn off all your electronics if you do not have a main power switch.