A 36-volt trolling motor requires special wiring between three 12-volt batteries in order to run properly. Three 12-volt batteries wired in series will put out 36 volts while maintaining the capacity rating of one battery.
Items you will need
Three 12-volt trolling motor batteries
Wire cutters
Wire eyelets
Wire
Place the three 12-volt batteries in your boat's battery compartment. Orient the batteries so that the negative terminal (-) on battery one is close to the positive terminal (+) on battery two, and the negative terminal (-) on battery two is close to the positive terminal (+) on battery three.
Attach a wire running from the negative (-) terminal of the first battery to the positive (+) terminal of the second battery.
Attach a wire running from the negative (-) terminal of the second battery to the positive (+) terminal of the third battery. The remaining two terminals should be the positive (+) on the first battery and the negative (-) on the third battery. These two terminals will now output 36 volts.
Attach wires to the two remaining terminals and to your 36-volt trolling motor's controls. Incorporate the appropriate fuses in your wiring as recommended by the MotorGuide schematic for your trolling motor.