Sorry - I think I missed the 2nd line of your first post....
"Do program each site as a different system ?" - maybe. Depends on the system, radio model, and possibly other factors.
Like any other multi-site system, you'll probably only want to try and monitor the closest site. Some of these business systems span not only numerous counties but even numerous states.
If you are appending from the main database in Sentinel, then these will include all the sites and TGID's, as Troy mentioned. They would also include the location information from the database, so that if you're using a GPS, they will enable when in range, and go back inactive when out of range, as does multi-site P25 or other type trunking system.