GaBoy, It sound like you want to use this just for your trolling motor. If so connect the pos of one battery to #1. Connect the pos of the other battery to #2. Connect the positive lead for the trolling motor to the common. Now connect the neg side of both batteries together and connect the neg lead from the trolling motor to the neg post of either battery. With this set up you can run your trolling motor from either battery or both. The manufacture of the switch just assumes you are going to use his switch for starting purposes, thats why they mention starter. They need to start thinking about us minorities. (crappie fisherman). Hope that helps.
Fair Winds and Following Seas
Bill H. PTC USN Ret
Chesapeake, Va