Here is the model of the battery switch that I use.

PERKO Inc.

I hook mine up like figure 1

http://gator49.hostgator.com/~zeromy...(8500INS1).pdf

The only difference is to hook the trolling motor directly to Battery 1. The switch connects Battery 1, Battery 2, or both to the Motor for starting/charging.

This way you can use either battery 1, 2, or both for the mains, troll with battery 1 or both, charge either 1 or 2 or both from the main motor.

It also allows you to run the trolling motor off of one battery and electronics off of the other if you have interference problems. Most interference problems can be solved with proper grounding or power filters from the trolling motor manufacturer.