Theres' some really good posts on here with people doing dual batteries. Most use a All/1/2/None switch from West Marine I think. Works so that you can isolate one battery from the other or run both while running so they both get a charge. Also works well when running a stereo when stopped so you don't drain your starting battery.
A quick search of the Modify forum will bring up several recent posts for you. It's one of my next planned upgrades after I add my LED lights so all my "accessories" (radio, LED's etc.) will run off the 2nd bank.