Good advice. Charge them separately or, better, use a Xantrex EchoCharge or a Balmar DuoCharge device (NOT a battery combiner or an isolator, etc.).
Sorry, halekai36, while I very much value your expertise and thoughts on many things, I have to disagree on your philosophy re: starting batteries.
The preferred setup is:
1. ONE large house bank, charged by every onboard device (battery charger, alternator, solar, wind, generator, etc.);
2. ONE starting battery, sized for your engine and NOT a deep-cycle battery; and
3. an EchoCharge or DuoCharge device, as per above.
This gives you a near bullet-proof, very efficient setup, and provides all the safety and redundancy you need.
Switches, fuses, breakers, etc. are a related but separate topic.