Is the engine on during this situation? If so you have an isolation/auto charge device that is either bad or connected incorrectly. if the engine is off then there is someting in the instriment panel/engine wiring/3 way switch that is incorrect.
I think you are going to find that there is no "wiring diagram" that is your boat's wiring unless you make it yourself, which I recommend. There is so much variation in boat wiring that unless we know what devices are in the circut we will be giving incorrect advice.
Welcome to the club of inadvertent electrical workers.
The house batteries should have + to + and - to -, and that must be the way it is or you would see large sparks and flames, adding another battery to that system is simply two cables that connect + to + and - to -. The fun begins when you want to isolate that "start" battery form the house bank. Add a switch (3-way) and you have to remember to switch to "both" to keep the starter battery charged. This is so much of an inconvienance for most that they HAVE to have an automatic device that automajically connectes the two banks when the alternator is producing power and disconnects them when it is not. There are about 5 different concepts on how you do this "correctly" and they all work.
If you can identify what (if any) isolation device you are using that would be a start point to getting your system fixed.
