Hello Dale,
To use a three manual sample set from a two-manual console you could either:
a) Simply auto-detect the third virtual manual to one of your MIDI manuals in addition to the other virtual manual that's already auto-detected to it (i.e. so that it always plays both simultaneously). Or:
b) Play the third division solely via couplers. Or:
c) Use Hauptwerk's 'floating divisions', which allow you to 'flip' a MIDI manual around dynamically amongst several virtual manuals.