Hello Mark,
The latter - organ definitions are completely separate from MIDI settings.
In the current version of Hauptwerk (v3.30) the procedure is:
- Unload the organ if it's loaded.
- Insert an entry for each external rank on the 'General settings | MIDI output paths' screen, specifying the appropriate MIDI port and channel for each.
- Insert an entry for each on the 'General settings | Rank MIDI outputs' screen, selecting the corresponding MIDI path (port/channel).
- Load the organ.
- On the 'Organ settings | Connect organ ranks to rank MIDI outputs' screen select the corresponding rank output entry for each external rank.