see
www.hellroaring.com for more info... I'm certainly no expert.
I think it depends on what you want to do. There are two basic configurations from what I understand:
1. Accessory Battery
2. Alternate Battery
The Accessory battery is supposed to be used to run all the accessories (usually an audio system) and has an isolator run between the main battery and the accessory battery. When charging, both batteries charge. However, when running the accessories, the acessory battery is isolated from the main battery so the main battery will not discharge, leaving it fresh for cranking your engine. In summary both batteries are always isolated except when charging. The acessory battery would have to be disconnected and connected to the main battery leads if you had a dead main battery. This is what I'm running.
2. Alternate Battery. Both batteries charge as in the accessory battery case, but the alternate battery is isolated in the sense that if the main battery is dead, you can switch to the alternate battery for cranking. All accessories run off the main battery.
FYI: Some people run a thing called a perko switch that allows them to run an accessory battery, with a manual switch that can switch to the acessory batter if the main is dead.
see
www.hellroaring.com for more info... I'm certainly no expert.