If you add a MPE panel somewhere in your HISE window, there will be a help button which opens a extensive documentation how this works.
The bottom line is that MPE modulators work a little bit different than usual modulators because they are supposed to be controlled via that panel from the end user - just drop MPE modulators on any place you might want to offer and the end user can activate and control them using the MPE panel - also people who don't have MPE controllers usually don't care about MPE so there has to be a global kill switch for this system (which is the MPE bypass button on the MPE panel).
The system is working perfectly in HEXERACT, so if there's anything weird in the usage let me know.