firstly, the Prophets already respond to polyphonic aftertouch. If you send it Poly Aftertouch, it will use the Aftertouch modulation on a per voice capacity, but if you send it Channel Aftertouch it will use it across all voices.
As for MPE, the MPE menu allows you to configure what CC74 will modulate, which is commonly what MPE uses for "Y-Axis" modulation. For example the Linnstrument uses up / down on the individual key as a modulation source (that is to say where you're pressing the key on the top / bottom of the key, not pressure).