Glad to hear you got it working. I’m not quite sure what you mean, the mappings can be made using the pedal or the software. I just tested this and it is working correctly.
In H90 Control, go to Control Assignments > Performance Parameter Mapping, select P switch > Parameter: Act/Byp > Control Source: Aux Switch #4. This will make the switch act/bypass the Program. Make sure you save the Program when you are done.
You can also go to System > External Control and map this globally so the aux switch does act/bypass for every Program.