The most common set up would be a total of 3 batteries in the boat. 1 start battery and 2 Deep Cycle batteries connected in series. Hooking the two 12 volt T/M batteries together in series gives you the 24 volts needed for your T/M. Ground/Negative (-) from battery A goes to T/M while the Positive (+) from battery B goes to T/M. Connect the positive (+) on battery A to the ground/negative (-) on battery B. If your wires going to the T/M are color coded, the red or red stripe will be the positive(+), while the solid black will be your ground/negative (-) Take nothing for granted, verify that on the T/M end, that color coded wires are matched correctly red to red/black to black. If both wires going to T/M from back of boat are the same color, you must use meter to verify which will be the positive (+) and which will be your ground/negative (-) This probably won't answer all your questions but is a start