I am not sure if this is possible but.....
The way the midi control changes are set at the moment means that you can assign a button (for example '1') on your foot controller to control for example stomp A. Lets assume that stomp A is set on a patch as the distortion. Now I go to another patch and press '1' and it activates the compressor because different effects can be added to each of the 4 stomp pedals. This is not very useful in a live situation as it means you have to know and remember during a song your signals change for each preset so that you you don't for example turn the distortion pedal on instead of a tremelo.
it would be very useful if each individual effect could be designated its own CC#, so that their position on the midi controller will remain fixed.
Hope this makes sense.