I have an older MC8 , but maybe this might be of use:
On a pop sessions gig, i have each of the 8 switches for different Scenes on the FM3 , I keep Tuner/Tap tempo on the Fm3, and usually have 1 button for the 'base' or the single/main preset
Think of having backup switches on the FM3 , so you can do some easy switches/toggles from there, don't completely rely on the MC6pro for everything, even though it certainly can get the job done, having the 'get out of jail free' card button on the FM3 is useful =)
Use the toggle mode on the FM3 and also on the MC6pro , ie. hit a footswitch it goes to a scene, hit it again it goes back to say your main scene
again this depends on your use case/setup and effects
In my metal band otherwise, i have it setup in a similar way, except for one track so that's on a separate preset on the MC8
another way of using the MC6 is say in a song setup , so depending on the tracks you play, you have a main view /preset and you can then jump to a preset on the MC6 for that song, where all 6 footswitches are setup accordingly
and then you can switch /go back to main view, repeat
I since only use the MC8 for sessions as the metal band is all with midi/laptop changes,