Hello Wayne,
(I don't have first-hand experience myself with an Allen MDS organ.)
In order for a digital organ's pistons to be usable with Hauptwerk they would each need to send unique and constant MIDI messages that Hauptwerk can recognise (e.g. MIDI program changes, with each piston using a different MIDI program number and/or MIDI channel and always sending the same message). On some digital organs you have to select a "piston mode" (or similar) within the digital organ's firmware menu in order to enable that. (By default many digital organs instead either send no MIDI messages from their pistons, or they send the current states of their stops after the piston has activated the digital organ's internal combination.)
However, it's important to be aware that you mustn't have both the digital organ's MIDI stops and its MIDI pistons auto-detected to Hauptwerk, otherwise the two combination systems will inevitably 'fight over' the states of the stops (see the "Playing Hauptwerk live from a digital organ" section in the main Hauptwerk user guide -- pages 272-273 in the current v8.0 version -- for more details).