Kevin,
A standard setup would include the following:
1. 24 Volt trolling motor
2. 2-12 volt deep cycle batteries (in series = 24 VDC)
3. permanently installed 2 battery 10A marine waterproof charger
4. 2 position % charge meter
You should end up with a 24 V plug/receptacle at your bow where you plug you trolling motor in.
You should use #6 gauge Marine conductors if you do the wiring yourself.
You should use good quality electrical connectors, heat shrink wrap connections, and always use SS fasteners.
You should consult an expert to check your wiring.
You should have the battery charger permanently connected to the two 12 volt batteries.
You should charge you batteries after every use.
You should know the state of your batteries, so do the next item.
You should install a battery monitor, such as a two position % charge meter by Altus.
You should have a 30A breaker feeding the trolling motor power. It should be accessible, if it ever trips, in heavy slop.
Hopefully, you have the room to hide all this stuff. Oh ya, neatness counts.
Good fishing,
BATMAN