Howdy,
I assume this is the system you are after:
ULS License - Public Safety Pool, Trunked License - WQBY325 - CHEATHAM, COUNTY OF - Frequencies Summary
As you mentioned, it has three different sites.
Think of a site as a ham repeater. If there are three sites, think of it like three repeaters but in different locations.
Now, with the trunked systems, each repeater location actually has multiple repeaters. The control channel tells the radio which input frequency to transmit on (i.e. which repeater to use); likewise, the control channel tells the receiving radios which repeater to listen to.
There are multiple sites (repeater locations) to increase the geographic area that is covered by the radio system.
Calls can be broadcast by 1, 2, or all sites simultaneously. The traffic might be identical on all sites, or there could be calls that are on some repeater sites but not the others.
If all of the traffic is identical on all of the sites, there is no benefit to monitoring more than the site that you can best receive. If there is something of interest on a different site but is not broadcast on your "home" site, then it might be useful to monitor more than one site.
When you did the channel order test, there are two possibilities:
1) The channels are actually the same exact frequency just duplicated in the scanner/EZ Scan. The basic Quick Import on Digital Frequency Search duplicates most trunked frequencies twice. The Advanced Quick Import will have an option to exclude the duplicate mobiles (once that feature of the website is complete).
2) You are picking up the same call on multiple sites. If the frequencies are indeed unique, then you are likely picking up the same exact call simulcast on more than one site.
If you go to the location tab of the FCC ULS license page, you can see which frequencies belong to each site.
The Station Classes are probably incorrectly done on this license. They should be either FB6/MO6 or FB8/MO8. This is the case with a lot of licenses. Since the licensing is sloppy, I err on providing duplicate data on my website rather than suppressing useful frequencies. I do not suppress mobiles (MO), because many MO frequencies are of interest. On the other hand, trunked system input frequencies are not terribly useful. But I can't suppress them if they aren't licensed properly.
Also, program 453.3625 separately. It looks like a talkaround/tac frequency for the county court or jail. It should be NXDN.
I would put each site into its own scanlist. There is a bug with EZ Scan. Sometimes they don't move scanlists correctly. If you go to the scanlist tab and open the scanlist setting, then close it again, sometimes that moves the frequency to where it is supposed to go.
As an example, here is how I would organize it (channel order is made up below):
Scanlist 10: CCSO ASHLND NXDN
460.275 Channel 1
460.3625 Channel 2
460.575 Channel 3
Scanlist 11: CCSO PLSNTV NXDN
453.4875 Channel 1
453.7375 Channel 2
460.6125 Channel 3
Scanlist 12: CCSO KNGSSP NXDN
453.6875 Channel 1
460.3375 Channel 2
460.625 Channel 3
Scanlist 13: CCSO Court/Jail
453.3625 CCSO Court?
All of these would have a Mode of NXDN, "any" NXDN RAN value, and 0 for talkgroup (any).