I use a similar strategy.

I use a Rocktron MidiMate. I have it set up so the bottom five buttons allow me to choose a preset (so mine are banks of five as well) and the top five buttons set to toggle on/off:
DIST
MOD
DELAY
FX1
FX2

I set up my banks similarly:
clean
crunch
rhythm gain
lead
acoustic

My "acoustic" preset is one I found that makes an electric sound like an acoustic. It's not perfect - but close enough. I play at my church. We typically play 4 songs per service. I may play one on acoustic. It's a lot of extra effort to bring in an acoustic guitar and set up another channel for it so I just flip to the neck pickup and use this acoustic preset. It's close enough, especially in the mix of the band, to pull of one song.

Back to organizing - I have modified the above approach a little lately. I've used the three gain slots to just be different gain tones - typically getting heavier gain as I go from left to right. I used to create lead presets which were copies of the preset directly next to it but just "more" (more gain, delay/reverb, volume, etc). I stopped using this approach and have gone to using a boost in the FX Loop via a Line6 M9. It's a more natural transition between rhythm and gain this way as the 11R doesn't trail any effects when you change presets so I had some unnatural hard cuts on some songs. A bit off topic - but thought I would share as it's changed how I organize my presets.