Yes the ideal set up is one start battery for port eng., one start battery for starb eng., and deep cycle batteries for a house bank all isolated from each other. I agree typically it's likely your port battery is used for house loads however if I recall correctly, the port engine also runs off that port battery, and both of the batteries are paralleled together during cranking which IMO is not ideal as you are then cranking off the deep cycle house battery if that's what you have for the port battery.
If this is the setup you have, I'd be doing the following:
- ensure both of the current batteries are crankers/start batteries
- leave the current engine battery hookups alone
- add a house bank (1,2,3 batteries etc.) and hook up a negative cable to the existing batteries or engine block. for the same footprint, two 6 volt batteries will typically give you more capacity unless you go with higher priced batteries like Surrettes or other battery designs.
- find the house load positive cable that would go to the 12 volt electrical panel. This cable may currently go directly to one of the batteries or be picking up power somewhere at the helm. Disconnect this cable and hook it up to the new house bank.
- To charge all banks while maintaining isolation, get an isolator or similar multi bank charging device like an ACR. Ideally, you want one that allows you to hook up both alternators so look for 2 input/3 output. This provides an added back up, should one alternator fail, the other will still charge all banks:
http://www.allbatterysalesandservice.co ... ,2927.html
or
http://www.promariner.com/en/23127
or you can simply add and isolator or ACR for one engine to charge both engine batteries. Don't hook up an ACR to an engine battery and house battery. Ideally you want the same battery type on both sides. The other engine can be hooked up to charge the house bank. This ACR would be good for one engine to charge both start batteries. It can also be controlled from the helm with a remote switch and also has the added feature of a manual on/off switch on the unit itself so a separate battery switch is not needed. There are other less expensive models.
https://www.bluesea.com/products/7622/M ... 2V_DC_500A
All the options above require that you remove the alternator charge wire from it's current location and hook up directly to one of the above devices.
- you'll need a 3 bank 120 volt charger for shore power charging. If you only have a 2 bank charger, you can utilize the same units you install for alternator charging (no additional ones needed).
- go through your wiring at the batteries and at the helm and make sure there are no accessories hooked up to starter battery power. If there is, move it to the house bank source. After you think you have all the wiring rerouted, disconnect the engine batteries and turn all the 12 volt accessories on. If something doesn't power up but it does when you hook up the starter batteries again, then that accessory is hooked up to one of the engine banks and should be rewired to the house source.
- with a meter, power up the house charger (shore power charger) and ensure all batteries are being charged. Shut charger off, start engines and check again.
There's a few considerations along the way but this gives you a basic idea of what's involved. Sounds and looks a lot more complicated than it really is and you'll have a lot of help here if you need it.
