Hello John,
in the organ-file within the stop-definition (and also with other thinks like couplers or tremulants) there is a command:
StopControlMIDIKeyNumber=
Here you can give the number of the key, which should switch this stop on and off.
At my console, the switches start with Number 36 (the notenumber for the great C, normally the lowest key). If i want to use this switch for this stop, i have to edit the organ-file and insert the line:
StopControlMIDIKeyNumber=36
You also have to set up with the Hauptwerk System Setup the "Stop Control MIDI Input Device" to the channel sending the data for the stops. This is set up by default to MIDI-channel 5.
With best regards and hopefully success - Martin Dümig