FWIW, I have found that a good single battery does quite nicely as long as all your components are up to the task. Conceptually I like the idea of multilpe batteries, but I have seen several dual setups fail. I like to keep things as simple as practical for each system.
A single good battery such as a big Odyssey or Optima battery would probably be enough for most situations. However, a dual set-up gives a fail safe or a reduntancy to your electricl system that can pay big dividends especially if you like to camp or travel.
This battery (http://www.odysseybatteries.com/battery/pc2150.htm) is the monster I use as my aux and to power everything but the chassis. It could do everything by itself, but if I leave it running when I am camping and run it down (it will take a deep discharge no problem) I have my Optima to get me started.
Again, my alternator charges both with no issues.