I should not matter what kind of pedal you are using. Any footswitch will work. To properly answer this question, it depends on exactly how you are doing this. From your note, it suggests that you are staying within the SAME setup, just doing a program change on one of the Zones. Is this correct? If so, rather than do a program change, simply do a MUTE/UNMUTE (TOGGLE MODE not MOMEMTARY) to turn on and off different zones as needed.(posted 9167 days ago)Otherwise, I'd suggest setting the pedal to the DATAINC parameter. This will simply move you to the next available setup. From SETUP 200, to 201 for example.
Hope this helps, Mike