Do you know what to expect? I mean have you ever used FRFR before, or recorded guitars and listened to them on studio monitors or anything like that? If you already know that you’re going for a good FRFR sound and not trying to have your FR setup sound & feel like a traditional guitar cab, then you’re probably 80% of the way there.
After that...I would say spend the majority of your time finding the right IR, then make small adjustments from there. If you’re having to really tweak the absolute hell out of everything, then chances are you can find a different IR that will get you closer to your sound and require less tweaking.
Most people tend to use the cab block hi/lo cut, somewhere in the range of 80ish & 8000ish. Other than that I don’t think there’s very many special tweaks that you really need to follow to get where you’re going...just set up your amp tone to taste and roll with it. Graphic EQ is a really useful tool, you can use it in the amp block, or a separate EQ block, or the global out...the differences really just depend on your application rather than any hard & fast rules.
For the Matrix, I think the general rule is to max the volume out or maybe set it around 3-4 o’clock, then use the AxeFX output knobs to control your volume. I’ve never really delved in to find out why that is, but I remember reading a few posts that its something about the circuitry that just makes a big difference on those amps once you cross a certain threshold. Personally I just leave the knobs dimed and control all my volume from the axe...works perfectly for everything from whisper quiet to blazing loud.