You've probably copied the entire system, rather than department(s) in your process. You can copy just the Department "stuff", being sure that location information is also included.
In a nutshell, here is how things work in a TRS with multiple sites: The scanner goes to Site 1, looking for the active control channel. It listens for channel grants, which is the talkgroup and which voice frequency to use. When it gets that channel grant information, it notes the TGID. From there, the scanner goes to your Department lists to see if that TGID is there. If so, the audio opens up and the scanner does its thing.
If there is no channel grants, or there are channel grants but none are in your Department Lists (or scan list), the scanner proceeds on the Site 2 and does the same thing.
This keeps going on in circles until all the sites are checked. Then if you have more systems or other stuff to scan, the scanner moves on to what is next.
The key thing is to not scan the same site or duplicate the site in the same system, unless you deliberately want to give preference to a certain site. The preference thing would come in to play if you know your most Favorite talkgroups are on just one of several sites.