I have the same problem. I prefer my amps gain channels. When I use the amps foot switch to go from a gain channel to clean I also have to hit a corroponding scene foot switch on the m13.

I don't know of a way around it.

There are some songs we do forwhich I have to use m13 distortions so that I can use 'latch mode' scene switching and cut things down to one switch. I'd be doing a tap dance otherwise.

My base setup (row a) I have now almost the same for my clean scene and distortion scene, anything fancy I add in at the time (live) by hitting the scene switch again to show the 12 effects for the scene. I have favourite less commonly used effects in row b and c.

This way I can change from clean to distorion on my amps footswitch as the base sound for me is the same (chorus, delay, reverb)