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.
I would even make a stronger statement: this is not the preferred setup, this is the only setup that works over the long run. The 1+2+1 switch is a solution that has flaws (some of them reported here) and over the long run one is going to forget putting the switch in the "House" mode after a charge session in the "Both" mode (I know there are a few of you out there who will never forget!). There are other considerations such as the inrush current when combining dischared and charged batteries, the fact that the charging current does not "balance itself", etc etc which makes the 1+2+1 a bad design choice.
Battery combiners have most of the flaws of the 1+2+1 switch except that they cannot be forgotten in the "Both" position. That's an improvement.
I use the Balmar DuoCharge and it works as advertised.
FYI, I also have a secret way of combining both banks but it is not accessible from any panel.