I play three or four nights a week with several different cover bands, and do a couple of regular duo and trio gigs, including a Jazz brunch on Sundays at a restaurant. None of the bands rehearse, so I've never had to make custom patches for specific songs (meaning I also never get the chance to tweak my patches in a rehearsal room with a band either, which can sometimes be frustrating).
Except for a few specialty, one-off kinds of patches, I have all of my patches set up the same way. They're distinct from one another by genre: "Blues," "Funk," "Country," "80s," "Classic Rock" and "Jazz," plus "Basic 1" and "Basic 2," which are all-around workhorse patches (I choose which one to use based on which guitar I'm playing and how the room sounds).
I have my MFC set to 0 bank size, so that I change patches with my bank switch. I use six scenes per patch:
1. Mild - usually cleanest setting, depending on the patch--on some, it means "closest to a normal tone")
2. Medium - usually crunchy, gain-wise, but can mean something else (see above)
3. Spicy - you get the idea
4. Dry Mod - depending on the patch, something with a combination of effects, but without much reverb or delay. For instance, in my "Funk" patch, the Dry Mod scene is a Mutron filter sound combined with compressor and a lower octave pitch block.
5. Wet Mod - generally a spacey, ballady combination of effects
6. Lead - Gain depends on the patch; it's high-gain for my '80s patch, clean for my Country patch, and in-between for my Blues patch.
The bottom row on my MFC is scenes 1-5 (scene 6, my lead patch, is on the top row, next to the tuner/tempo switch). The rest of the buttons are set up like a pedalboard--Comp, Drive, Phaser, Chorus, Delay, etc.
I also have an external switch set up as a boost, so that I can use anything for a lead sound, if I want to.
General rules:
I try to include unused blocks for every effect that's represented by an IA switch in every patch, so I don't "lose a pedal" from my virtual pedalboard when I change patches.
for my two "Mod" scenes, I usually use effects that aren't represented by the IA switches (most often using X and Y, but when necessary, adding a new block); that way, I get the most tonal mileage out of each scene.
This tends to work for me...