For what its worth, I run a dual battery setup in my boat. Granted, I dont have a winch or anything wacky, but its extremely simple. The switch cost $30, it has positions 1, 2, both and off. 1 uses battery one, 2 uses battery 2, both will use both. For a jeep (or other offroad vehicle), it might be a good idea to use a starting battery (high CA for starting and running), and then have the second battery be a deep cycle, which you use for winching, or lights, or whatever else, especially if you plan on using this battery while the vehicle is NOT running.
A starting battery can only be drained so many times before it dies. A deep cycle battery is designed to be drained down and recharged repeatedly.