Yes they charge and discharge as normal, however they are not linked so one is not going to boost the other for starting. If you needed to boost the primary battery for starting, you would have to use large jumper cables to connect them. Under normal use, the secondary battery will be maintained in a charged state, but will not discharge unless it is connected to the trucks electrical system somewhere. The problem with connecting it to the trucks electrical, is you can then have parasitic leaching of power around the isolator.
Usually an isolator is used to keep both batteries charged, while having a second battery that is used for things other than starting. For instance, my dual battery setup will have the primary running the starter, and most of the trucks electrical system, while the secondary battery runs the winch, and audio/video systems. This allows me to run my audio/video systems with the engine off, but never drain my starting battery. It also allows more amperage to go to the winch, while the trucks systems are maintained. I could theoretically run my A/C, while still winching, and have no power issues outside of the alternators ability to keep up with the charging requirements.
If you want to be able to connect the batteries for a boost type system, talk to Ryoken about the proper way to do it. His is setup so that he can run off of each battery, or combine them for heavy draw applications. (I may be wrong on this, but it can be done with a relay type system)