I've mentioned my general scheme before, but it is:
FLs are regional - usually consisting of about 9 counties. I currently have FLs covering 3 states. The first digit of the FL is the "super-region" - which is defined as a group of 9 FLs, and the second is map-based (get to that in a moment). I also have some FLs that are service-based, such as FLs 91-99 which are for Hospitals, Utilities, Schools, Services (ITINERANT, FM, MURS, CB, Air, RR, Ham, Marine, STORES, MALLS, ROAD CREWS, TOWING, NEWS, SECURITY, AIRSHOWS, Etc.)
So, yes, my channels are duplicated - I can access them by region or by service depending on what I want to monitor at the time. I can monitor all channels in an area, or all RR channels in many areas (basically all RR channels in range) to find new active channels.
The Systems in each FL are unique to each County, and have a map-based quick key (1=NW, 2=N, 3=NE, 4=W, 5=central, 6=E, 7=SW, 8=S, 9=SE, 0=regional). If an area has a trunked system and conventional channels, they are enabled/disabled with the same Quick Key.
I do have one county that is large enough to warrant a single FL, and in that case the 1-9 represents grids of that single county (NW, N, NE, W, central, E, SW, S, SE, regional).
My Departments (or Groups) are organized under each System as follows:
1 POLICE
2 FIRE
3 EMS
4 STATE
5 PW
6 HAZMAT
7 EMA
8 INTEROP
9 OTHER PS (SO / JAIL)
0 UNCONFIRMED PS
11 DEPARTMENT STORES
12 RESTERANTS
13 FAST FOOD
14 THEATERS
15 GROCERY STORES
16 MALL OPS
17 INDUSTRIAL
18 SECURITY
19 OTHER BIZ
10 UNCONFIRMED BIZ
21 MEDIA
22 AIR
23 RR
24 MARINE
25 TRANSPORTATION
26 ATTRACTIONS
27 COLLEGES
28 SCHOOLS
29 HOSPITALS
20 UNCONFIRMED SERVICES
31 UTILITIES - POWER
32 UTILITIES - GAS
33 UTILITIES - WATER
34 UTILITIES - CABLE
35 UTILITIES - TELEPHONE
36 FM
37 AM
38
39 HAM
30 UNCONFIRMED UTIL
41 FEDERAL
42 MILAIR
43 PARKS
44 VA
45 NATIONAL INTEROP
46 GMRS
47 FRS
48 MURS
49 CB
40 UNCONFIRMED FED
Quick Keys 51-99 are for Sites on Trunked Systems with smaller ones only using 91-99.
You may notice that like users are grouped together - 0-9 is PS, 10-19 is Business, 20-29 is Services, 30-39 is Utilities (with some others to fill the space), 40-49 is Federal with others to fill the space). Again, it's all about organization to help keep things easy to remember.
Obviously, some Departments are blank in many Systems, such as the CB list. I added it for completeness and expandability.
The number in front of the Department/Group tag is the Quick Key for reference. All my FLs, Systems, and Depts/Group use prepended Quick Key numbers. It helps remember what is what, and if I am using QK 44 and moving east, I know the next one to enable will be 45. If I were going south, the next one would have been 47. So, as long as you know the general direction you are going, remembering all those Quick Keys is trivial.
Obviously, this list is optimized for an x36 series scanner, but I do something similar with other scanners - both Uniden and GRE.