Kohldad,
You have a very common problem, so, do not be surprised that there is a good solution at hand. I installed a few of these before the depression killed our boat work business.
Go To
Yandina and scroll down the page. There are two models that could work, but the 100 amp has wires that can't be shortened and that is why you might consider the 160 amp version. Either will do. Read the downloadable manuals before you decide.
These devices are interesting. When charging power exists, it parallels the two batteries. When the voltage drops below charging levels, it separates them. They require no other modifications to the existing systems.
Matt