Listen to Onaquest.....
A: Get the design/builder's diagrams as soon as you can. Keep a set in the coach. It would also be good to get the chassis electric diagrams if you can. That may be difficult.
B: Find someone that can work on this stuff if you don't feel capable. The OE setup was done the way it was for a reason.
Unfortunately, if your current connections are anything like what you describe, then some PO has done you no favors at all. You should get it corrected as soon as practical.
Just so you know, a marine starting battery is just a plain old car battery with a more expensive label. A deep cycle battery (most common in electric golf carts) is a different animal. If the two are strapped together, the starting battery will be hard pressed to get charged to full density and if the bank gets run down as far as the deep cycles can go, your starting battery will be damaged.
Back before the depression, I did a lot of work on expensive boats.
Before the depression, I did a lot of boat work (why I bought the coach) and I saw this sort of foolishness all the time. (And provided repairs as considerable cost.)
Matt
