If you have the time, when you get your unit, spend some time auditioning every single preset and every scene in a preset with all your guitars and take notes. I built a spreadsheet listing each preset and I've gone through the entire list with my Les Paul and now I'm repeating the task with my strat. What I find is there are certain scenes I may like in a preset, but not the others. Also, when playing a scene, have FM9 Edit running and turn some things on and off. You'll see there are effect blocks in the preset that are always bypassed in all of the scenes. Try engaging them and see what happens. Also, many of the effect blocks like reverb, delay, drive, chorus, etc. have multiple channels. Try using different channels. You may find a sound that you really like that isn't one of the defined scenes. When you encounter something that surprises you, try and dive down into the block definitions to figure out how the sound is made. You'll learn a lot doing this. I never did this for any other multieffector/modeling unit I owned before because the presets were all so lame. It is worth doing all this with the Fractal units.
When you figure out your favorite sounds, edit that preset/scene and save off the block definitions to your block library. Then when you go to build a preset you can just call up the block definition and get the sound you want.
I have an FM9 T and love it. I use it at church and have gotten nothing but compliments. The sound guy has finally discovered I sound good and I can play and has turned me up in the mix (if you play at a church you'll know what I mean - for some reason you can never hear the electric guitar in the mix at a lot of churches). The unit is a joy to play though. Take the time to dial in your tones.
Thanks for the information, I will try implementing that method to get familiar with what's available and find what will work for me, that's a great suggestion!
I'm a minimalist with effects, I like a good ambient Reverb that I can vary the length and amount applied as needed and a spring reverb at times. Two or three varieties of delays and a couple of od stomps and I'm good to go. I wouldn't be using that many variants on one rig, probably just one of each effect, I like to limit my options or I won't spend much time playing.
As for guitars, I made that scenario a little simpler for myself last November and December. I had three electrics and liked each one, but they weren't interchangeable for me. I was dealing with the same situation you stated, not every rig I was using sounded good with each guitar.
I also struggled when switching guitars, each neck was different, and unlike many other players I can't go from one type of neck to another without fumbling around. I bought a new guitar in November and played it for a few weeks, it will cover any type of music I might play. So I sold my other three electrics and bought a second matching model guitar as a backup to the new one, just in a different color.
I haven't played electric guitar in a live environment in almost three decades when I moved from stage to front of house. I've taken a break from foh and want to start playing live again.
And yes, I'm very familiar with churches and their approach to sound reinforcement. I've done audio/video installations in church's throughout the Midwest and Southeast since the mid 1990's, I stopped doing that this year, I'm getting to old and to tired. But I've been invited to set in sometime at a church with their p&w band, maybe get to it in early summer.