I'm kinda surprised it works at all on 12v. Is this Larry G.'s old Lund? I'd expect better from his dealer of choice, but a lot of the rigging is done by minimum wage types. Kim's Smokercraft had the TM harness disconnected from the battery harness, for instance. It wouldn't have taken much to check for power, and a .5 second blip on the TM won't hurt anything, either.
Not sure what wiring scheme you have, but my boat had orange and red wires, two each, one of each from bow to each battery. I wish they'd used red & black, but it doesn't matter, of course. What I did was hook both orange wires to the negative pole on one battery, and both red wires to the positive pole on the other battery....all while both were unhooked from the bow panel. Both orange wires connect to the negative side at the bow panel, both red wires connect to the positive side at the bow panel. As I recall, the +/- marks are actually on the plug, not the receptical. Then, you need a jumper wire to connect the positive pole of the first battery to the negative pole of the second battery. I got mine at the auto parts store...B&B, probably. This puts the batteries in series, so 24v. The reason you double up on the wires is because they'll carry twice the current and reduce the electrical resistance, so don't get hot and cause yet more resistance. Or fires.
I'd suggest circuit breakers instead of fuses. Circuit breakers don't last forever, either. If you are on TM because your big motor is TU, and you blow the fuses, you can be in deep trouble at some lakes, in some situations.
Assuming you have an onboard battery charger designed for at least two batteries, just hook the pairs of leads to one battery per pair. They are designed to do that, and it works fine, highly recommended. Give me a jingle if you need more help or info.
C&R, Steve