I ran a 12 volt minn kota powerdrive ipilot for 2 years with 2 batteries wired parallel , but what I did and it will give you a better run time a less drainage on the batteries was used both batteries by hooking the trolling motor positive to battery A and the trolling motor negative to battery B,
now it looks like one big 12volt battery to the trolling motor !!! and like Speck said hook the charger up positive battery A and negative to battery B now you are charging both batteries at the same time and rate !!!

