Re: Charging system on 1999 Bayliner Capri?
Using the standard Off/1/2/Both type switch does not isolate the systems, only which battery you are using. In position 1, you are using battery #1 for everything. When running, only battery 1 is being charged. When in 2, battery 2 is used for everything and only battery 2 is being charged. In the Both position, both batteries are basically tied together to make a single battery and both are charged.
To completely separate the House and Engine systems to use their own battery and the engine charges both, you need something like this.
Blue Sea Systems Add A Battery 7650 - iboats
You turn it on, both systems are completely isolated from each other. You can not run down your starting battery running your house system down.
When you start the engine, the automatic charge relay combines and charges both batteries.
Here is some more info on the add-a battery.
Add-A-Battery - 120A - Blue Sea Systems