Mike, I just got the FM3 yesterday and I'm a Jazz player. It is a beautiful unit for jazz. Here is my input. That's a great simple beautiful sound the guy is achieving. Also, listen to Tim Miller and Kurt Rosenwinkel (modern jazz pros) when they are using the Fractal products with effects.
First, start simple with Input, Amp, Cab, Reverb, Output.
Amp: I don't prefer the Roland Jazz Chorus 120. They are too bright and thin sounding (it will work fine though if EQ'd to taste). Although, I'm not aware of any of my favorite players that use that amp for jazz, but to each his own. Here's what I've heard and seen on videos from the internet. John Scofield, Wolfgang Muthspiel - now seem to like Vox AC 30; Kurt Rosenwinkel - said he uses Fender Twin Reverb amp in the Axe FXIII; Pat Metheny - uses a Kemper Profiler now but has always used a Digitech 2021Preamp and Lexicon Reverbs; others uses solid state "High Headroom" amps from Polytone, Henriksen, DV Mark, etc.. I just got the FM3 yesterday, but I was able to quickly dial up great tone using any Fender cleans (Deluxe, Twin, Princeton, etc.), Vox AC 30, the PRS Archon (Archean) Clean model, The Dumble Clean etc.. The key is "headroom" like unix-guy said above. Turn the preamp volume down to about 2, Master way up and use the level for volume to taste (don't clip your mixer or FRFR speaker etc.. There is a "Headroom" meter on the page where you adjust these volumes. Watch it and see what happens as you change things. If you hear distortion, lower the preamp volume and/or raise the master. EQ it by perhaps raising Bass to 6 and lowering Treble/Mids to 4. Remove highs like DaveO said above.
Cab: Learning more about this, but as Laurent-G said, try using two Cab IR's. I tried this yesterday and it was great. You can Pan them, so it's like using two different cabinets, one for L one for R and hearing the IR's in stereo along with Reverb . . .
Reverb: This is where the FM3 shines over other competitors in my opinion. There are so many choices depending on what you are looking for. Try a Large Hall, Wide Hall, Rich Hall and turn the decay time up into the 4 sec range then back off the effect using the Mix control. Or, if you prefer use a Spring Reverb to sound less modern and more up front. The reverb tails are absolutely gorgeous. Play around with Reverb once you have a Clean, high headroom sound that is warm and not distorted.
Next try adding some Delay.
I've spoke to Tim Miller about tone on his forum and he said the Fractal products have great delays and verbs. We talked about the right settings. He said "I use several different settings for different situations. For a basic sound, I like the way spring reverb "feels" to play. With digital reverb, I tend to dial in a small or medium room and sometimes add a little of echo (delay) mixed in to the sound (approx 300-400 ms.) If I want more ambience I use a larger room reverb or add a stereo delay mixed in as well." That's great advice there, re-reading it I may try some smaller reverb rooms but I do love the tails on the larger halls in the FM3 and maybe for ballads they might work well for some players.
Mike Stern uses the heck out of chorus and gets a great sound (he could sound great on anything with his experience). If you like that sound, add Chorus, they are awesome in the FM3 as well.
Hope this helps, search the internet as well and think of the FM3 as a chain of real life "blocks" or devices. So much easier than it was years ago.
By the way, I have a Kemper as well, but I'm now preferring the FM3. It's small footprint is great for jazz gigs where there isn't much room and the 3 switches are enough if you learn about Scenes, Layouts and Views.
Dave