Deriving my comment on this system: http://www.radioreference.com/apps/db/?sid=7073
You should only use the Control Channels and don't worry about the base/offset, the data stream from the control channel will contain that information and the 396XT will store those automatically.
On a local P25 system, the only thing I entered was the control channels and the scanner picked up and stored them. But, I have a friend who has a Radio Shack Pro 106 (aka GRE 500) and he had to manually enter his offsets. That scanner didn't automatically store them, as well as anyone else around who had that scanner.