If your boat has a 24 volt battery system it probably has two 12 volt batteries that are wired together so that the negative post of the first battery connects to the positive post of the second battery. I bought a stratos boat and it has two 12 volt batteries ran in series to a 24 volt trolling motor.

Charging A Trolling Battery From Your Outboard
Hooking up batteries for 24 volt. If i hook up my electronics to one of the 12 volt batteries in the 24 volt system am i going to be pushing 12 or 24 volts to them when the trolling motor is plugged in. How do i hook up a onboard charger and how many bank charger do i need to buy. Using the same series process used with multiple battery flashlights you are able to connect two 12 volt deep cycle batteries together in order to make in essence a 24 volt battery that can power a 24 volt accessory like a trolling motor. Wire in series only as directed in wiring diagram to provide 24 volts. The 24 volt connection is the kind that creates the 24 volt system when the trolling motor is plugged in. Both the 24v and 36v trolling motor wiring diagrams are listed below along with the recommended circuit breaker.
Connect the negative lead from the multimeter to the negative terminal on the second battery. Never feed 24 volts into a 12v motor. The multimeter display will show a total voltage equal to the sum of the voltage of both batteries. Two 12 volt deep cycle batteries are required. These larger motors and multiple batteries are wired in a series pattern and optimally the circuit breaker should be wired within 4 of your battery. Make sure that the trolling motor is switched to the off position or speed selector set to 0.
Connect a connector cable to the positive terminal of battery 1 and to the negative terminal of battery 2. 24 volt battery series connection. Connect the neutral terminal of a battery in the first set to the positive terminal of a battery in the second set with a short piece of wire. If your charger is small enough to be carried aboard your boat you can leave these cables in place since the charging procedure requires it. Measure the voltage across the two batteries by connecting the positive lead of the multimeter to the positive terminal on the first battery. It is important to note you should never feed more voltage into a motor than what it is rated for ie.
24 volt systems 2 batteries.