There are a couple of ways to do this. The best way if you are going to keep your boat for awhile is to install a 24v recepticle. All you have to do after installation is plug in and go. if you have the 2 prong recepticle, you can get a 2 prong plug that is crossed to a 24v. Or you can use a 12 volt two prong system, and switch to 24v at the batteries.
Installing a 24v recepticle would be the best. I have installed motors using the other methods, and never had a problem.
With the 24v plug that plugs into a 2 prong recepticle, you will have 2 hot a one ground wire coming out of the plug. If you used your 12v system, run the hot wire to the positive of one battery and the negitive wire to the other battery. You would then run a jumper wire from the negitive of battery one to the positive of battery two. Using this system your two hot wires coming out of your trolling motor would be spliced together. Give me a shout if you have any questions.