It all depends how much you want to spend. If it were me I would do the 12v 55lb thrust Minn Kota Terrova with Auto Pilot and optima blue top battery and a CTEK charger. This set up will set you back $1300 ish + tax. As for choosing between 12v or 24v I would consider: how long you fish for when your on the water, do you use a separate starting battery for your motor, or is it pull start, do you intend to use the trolling motor to troll or just to position yourself.
I use one battery for starting my motor, fishfinder, and I use the trolling motor for 4-5 hrs continuously to move slowly while pickerel fishing and I have yet to run out of battery. Thats with a interstate battery. I don't like the added weight of another battery and I find for how long I fish at a time, it is not necessary.