If you want it to check multiple sites, the best way to do it is to program each site as its own system. It is a little annoying to have to deal with copies of all the talkgroups, but if you make a copy of the system after you get all the talkgroups straight, it's not too bad.
In my opinion, it's probably best to stick to one site and only the active control channel on that site, unless you are in a location with very little radio traffic. The more sites you try to have it decode, the more it will be jumping around getting a few frames here and there of various sites (and that's if you are lucky).
Where are you? What systems? What types, etc.?