There should be three terminals on the battery selector switch. The markings are usually 1,2 and C. I and 2 go to the batteries. It really won't matter which battery goes to which terminal 1 or 2, and these sould have the red wire (positive) from the battery attached. The black wires go to the ground bus. Which in this case is the engine block. The C terminal goes to to your power bus. A bus is a bar of metal which combines the inputs. This can be your starter or an actual bar might be found in the electrical panel etc.
This info is very general and could differ with your boats wiring. Without actually looking at your system this is an educated guess.