Schematic 2 is how my boat was wired by the factory/dealer. This is probably how yours is too. It represents the cheapest quickest way to install a second battery. The #1 battery is wired directly to the alternator and the charger output. The only way the #2 battery can ever get charged by either the alternator or the battery charger is when the main (battery switch is in the BOTH position. This of course essentially defeats the very purpose for wanting a second battery bank in the first place!) I wanted to have ....- one battery just for the engine and one battery bank just for everything else
- the ability in a pinch to use the house battery (or all the batteries combined) as a starting battery
- for this to work essentially automatically without me having to keep setting switches and remember what positions they were in all the time

The secret is a little rewiring and a battery combiner
http://www.westmarine.com/webapp/commerce/command/ProductDisplay?prmenbr=201andprrfnbr=7470).
This $65.00 gadget lets your charger or your alternator automatically charge both batteries as though they were connected together in one big bank. At all other times they batteries are controlled by your battery switches which mostly keeps them isolated from each other.

If your system is set up like in schematic #1, you need to make the following changes ....

1. Disconnect the negative cables from all your batteries while you are working on this. Batteries contain huge amounts of power and a short can cause burns, fires and explosions! Disconnect your shore power too just to be sure you dont goof.

2. Disconnect the house (12v DC panel) positive wire from the common terminal on the battery switch and connect it to terminal 2 on the
battery switch. Make sure the positive cable from the starting battery is connected to terminal one on the battery switch and the positive cable from the house battery is connected to terminal two on the battery
switch.

3. Get a battery combiner and follow its installation instructions. All
I had to do with mine was (from the combiner) run a wire to terminal 1 on the battery
switch, and run another wire to terminal 2 on the battery switch and then run a wire from the ground terminal on the combiner to the common
ground on the battery.

4. The battery switch now controls only which battery the engine is starting and operating off of. If you leave the battery switch in the
Battery #1 position, the engine will use only #1 for starting. The 12V house (12V DC panel) functions are all operating off Battery bank #2 all the time.
If ever necessary in a pinch you can start the engine using battery #2 or even both together by changing the battery switch. All batteries get charged no matter what position the switch is in.

5. You can make the system safer and better if you also add a switch for the cable connecting the house battery - otherwise the only way to disconnect the DC panel is to take the cable off the #2 battery terminals.
http://www.westmarine.com/webapp/commerce/command/ProductDisplay?prmenbr=201andprrfnbr=63168andstore_num=9andstore_name=Electricalandsubdept_num=457andsubdept_name=Batteries

After rewiring

Original factory/dealership installation