Jeremy,
There are two ways to hook up dual batteries for your trolling motor, parallel and in series. If the batteries are hooked up in parallel the output voltage would be 12 volts but your current availability and longevity should be greater, you could possibly charge both batteries off of one charger this way. If they are in series your output would be 24 volts.
You can tell by looking at the connections. Parallel will have both batteries (+) and (-) terminals hooked together and then out to the trolling motor. In series will have one batteries (-) hooked to the other's (+) terminal and then a (+) terminal fron one battery and a (-) terminal from the other battery going to the trolling motor.