I think you want to run them in parallel. In series you run the positive of one, to the negative of the other, and use the positive of the one not used in the battery connection to the positive of your motor, and same with the negative, but that is a 24VDC source. Parallel you run the positive of one battery to the positive of the other, same with negative, and then you can hook the positive of the motor to either battery positive, and the negative to either battery and you have a 12VDC source but with a LOT more reserve. If you have the room and want to really go nuts you can run 4 batteries, 2 in series and 2 in parallel to get a beefed up 24VDC source. Heck, you can fill your boat with batteries for that matter!
One battery is always going to work a little harder than the other, so using the same age, type, make, and model battery will minimize this and prolong the life of the batteries.