The more voltage you have the more amps you have available to run for extended periods of time. The 36 volt system is pretty much the standard these days for modern bass boats. You can have power all day in windy or current conditions.

The way you wire the batteries is by attatching the wire from the ground of one battery to the positive of the next battery and so on. The directions that come with the trolling motor should show you the correct way to wire the motor.

I hope this helps!