I have mine hooked up to all three of my batteries although i dont think you have to but better safe than sorry
Check these dual pros out...
http://www.dualpro.com/store/items/9/22/
they are factory reconditioned so cheaper than buying the brand new and same price as the mk 345... I was gonna buy another minn kota when my last one burned up then i read all the positive reviews about dual pro out there