Some boat manufactures wire with 4 wires (2 red & 2 black) to the front so that you can use a 4 pin plug, and charge from it. The 2 pos wires are usually through a 40 amp circuit breaker for each pos (red) wire. 12/24V motors use 3 wires (1 for common, 1 for 12V, and 1 for 24V). The way it should be wired if you want to charge from the plug is as follows. Use a 4 pin twist lock receptacle and plug. Lets call the pin with the locking tab #1 and clockwise from that pin #2, 3, & 4. Wire battery #1 gnd to pin 1, battery #1 pos to pin 2, battery #2 gnd to pin 3, and battery #2 pos to pin 4. On the trolling motor male plug wire gnd to pin #1, 12V to pin #2 and 24V to pin #4. Short pins 2 and 3 together. On the battery charger male plug connect the charger pos to pins 2 and 4 and the charger neg to pins 1 and 3. That will charge the 2 batteries in parallel. A 20 amp charger is recommended.
The above method has one disadvantage in that when the trolling motor is being used in the 24V position the wire that is effectively connecting the pos of battery 1 to the neg of battey 2 is about 40 feet long and since the current path is in series there is more voltage dropped over the long wire, even if it is #4 size and even more if it is #6 size.
The better method is to connect the pos of battery #1 to the neg of battery #2 at the batteries and only run 3 wires forward, but now you must charge each battery independently either with a 2 bank onboard charger, or 2 battery chargers.
I hope this doesn't sound too confusing, but it would be a lot easier to explain with the help of a diargam.
Russ C.