Well, the way I am doing this is using the preset program mapping in the midi section for my program changes. The ability to bypass in the program mapping was added in the new beta software. This give you the option to bypass by setting up one of your patches as a bypass to the unit, therefore not affecting the program change in your 2nd midi unit.
aka my midi pedal; 1 changes the eventide to 2:1, midi pedal 2 changes it to bypass, etc. This is by far the quickest and easiest way to do this.
By the way excellent job eventide!! I hope that you guys are working on a pedal form of the Eclipse for guitar!! I will be the first in line for it.