Well, there are three ways you could go about this. One, you could try to change the kinds of MIDI messages being sent by the footswitch. You could reorganize the presets on your H9 to fit the footswitches behavior, or you could reconfigure the H9's mapping of MIDI program changes to presets. I'd personally try reorganizing the H9 presets to fit the footswitches behavior because I think that's going to be the easiest to understand and most flexible solution.
If you save a preset in the active state, it will be loaded (by MIDI program change) in the active state. If you save it as bypassed, it will be loaded as bypassed.
I don't understand what you're saying here. What do you mean by this?