I've had me 396 setup a few different ways:
What I have now is a combination of both the below ways:
1. I have the P25 trunking (MMR) sites setup in groups on a key (90-99) so I can easily lock in an out a group of towers if they are losing signal. I then have Departments for Metro Fire Dispatch, Metro Ambulance, Metro Fire Fireground and Misc Ambulance.
2. I have a full statewide file for all sites with the full channel plan for each department. So let's say 32 is Metro Fire, I have all the Dispatch Channels, Fireground and Misc Channels, with every control channel for the sites they operate on in one big system. This is so that if I end up on the other side of town, where I may not have the local site programmed in, I can do a mass site search and lock in/out any sites that I need.
I also do the same thing for my non trunked systems as well, so in the case of CFA I have a key for each of the districts, so I can pinpoint one district only and where a trunking group exists I can have that on the same key. I also have one big master group that has all conventional channels in there, so I can recall up a fireground simplex channel or odd repeater channel if need be.
I find that the 96XT's load so much quicker than the x36 series so it's not a pain to load it up with a lot of data and lock in/out what you need. Sites can be locked out individually if need be or as a group. Only thing that is a pain, which the 436 addresses is that if you want to lock onto on TGID, you almost need to find the busiest site to lock onto or lock out all the other TGID and let it scan.
Also, I found it handy to create a system with the specific dispatch channels for some towns that I visit often, and my home location so I can lock in/out them when I get close and automatically be on the right channels for the area.