The way I did it was to program the different MSP sub systems (Zones) into their own sites. You can assign each site it's own Quick Key, and can even assign each Site a different start up key.
I then put all of the Talk Groups into their own Groups in the 996XT. I broke that down by Troop, so all of the Troop A TGs are in one group, all of the Troop B in another, and so on.
What TGs you hear will depend on which Zone you are listening to.
For example, in Zone 5, which covers the eastern MA/Greater Boston area, you will here all of Troop A, Troop E, Troop H, and some of Troops C and D. You won't hear the airport, Troop F, because they are on a totally different trunk system at Logan.
If you are listening to Zone 8, central MA, you will hear Troop C and Troop E, and parts of Troops A, H, and B.
How much you want to put into the scanner depends on where you are and where you plan to be. That's assuming this is going into your vehicle. If it's going to be used as a base unit, the programming is going to be different depending on where you are. I'm south of Boston, so I can hear Zone 5, Zone 8, and Zone 3 (Plymouth and Bristol Counties). That allows me to hear Troops from the NH state line, to west of Worcester, to the RI state line, and parts of the Upper Cape.
It's complex at first, because it's a statewide system, with the exceptions of parts of western MA which are still being built out. It takes a while to tweak the programming to get exactly what you want. In addition to the MSP, there are other agencies on the trunk that you might want to listen to.
There is some really good information at
Scan New England that will help you understand how the system is designed.
You didn't mention it, but programming is much easier if you use software than if you manually program.