I'm 2 months into my PSR-800 and had the same struggles. I'll start with a brief explanation but if it isn't helpful to you then feel free to so advise. And others with more experience will chime-in, I'm certain. First, you may want to refer to some much helpful replies that were given to my own post in January. Here's that link:
http://forums.radioreference.com/gre-scanners/257708-psr-800-confusion-multi-site-workaround.html
In its simplest form, I began by importing my desired system via the EZ Scan software. That import resulted in 7 sites. In time, I discovered there are only 3 sites that I only pick up due to my proximity to those various sites. And my only interest in that system is Safety. So given those two pieces of information, I deleted TGRP's that were of no interest (truth be told, when it all began to click a little later I did a fresh import by the "Standard" import type and selected the TGRP's of interest).
Once I had that system (with all 7 sites) with the reduced TGRP's I duplicated it twice, resulting in 3 systems that matched. Then I modified each of those 3 systems as such: I renamed each to match the site of interest (for me, one was West Alex, another was Dayton, and the last was Darke CO). Next, I deleted all but 1 site within each of those 3 systems. Hence, in my system named West Alex I kept the West Alex site and deleted the other 6 sites. For my Dayton system I kept the Dayton site and deleted the others... and used the same scheme for the Darke CO system.
Next, I named 3 scanlists to match the 3 system names. Then, within each system, I directed its TGRP's to the appropriately named scanlist (the TGRP's in my West Alex system were associated with my West Alex scanlist, Dayton TGRP's to Dayton scanlist, and so on).
For my needs, these 3 systems reside in the same V-Folder and I toggle the scanlists as needed. When I was first experimenting, I created separate V-Folders for each system but for my use it doesn't make sense to do that today and it's much quicker to toggle the scanlists on and off as needed. Also when I first started, I balked at this process of having to manually pick-and-choose sites but today it works very well for me and it is a simple and quick process.
Those more experienced will probably advise that the TGRP's don't need to be duplicated across all of the systems but I found it a little easier to set it up that way, initially, and I am not aware of any negative consequences in having done it that way.
Good luck!