Captm, let me know how this turns out. I am completely insure of how to set up a second battery and would love to see what you end up with. I was just gonna start a thread for this purpose till I saw yours. I wanted to add a battery in my 01 Tacoma for lights, roof vent, radio, and charging my electronics when camping.
This can actually be a very pain free process. A lot of people spend a LOT of money when they don't have to...
Basically you need to protect your starting battery, not with an isolator, as those will actually hinder charging unless you spend big bucks on one.
So, one way is with the Blue Sea 7622 like Captm is going to use. What this does is simple: It disconnects the batteries when the car is off. You don't want them connected when you're running your accessories in the back and drain BOTH batteries when the car is off, or you won't get it to start again! But you DO want them connected when the engine is running so that the alternator can charge both batteries. The 7622 can do this by tapping a 12 volt source that is only on when the engine is running, this way it disconnects the two batteries when the cars is off.
The 7622 also has a manual switch on it so that you can override. You might want to do this if your starting battery died, and you need to use the second battery to boost the starting battery so you can start the car. No problem, flip on the manual connection and there's your boost pack!
You can pick up a 7622 on ebay for $150.
The other thing is breakers. You want a breaker at each end of the wire between the batteries, 70 amps. Each breaker should be within 18" of the battery its protecting, the closer the better. If something gets the wire in the middle of the run, both breakers will pop, protecting each battery from short.