I use Hauptwerk all the time. I'm on VEP 6, but I think setup is the same.
- Open Hauptwerk and in organ settings go to "keyboards"
- Select a keyboard (great, swell, pedal, etc) and then assign "input" to "direct input from your MIDI organ console/keyboard/sequencer"
- Set "MIDI IN port" to "Hauptwerk VST Link"
- Set "MIDI channel" to "<channel whatever>"
- Repeat steps 2-4 for each keyboard making sure you put each keyboard on a different channel
- In VEP, insert plugin Hauptwerk VST Link
- In VEP, change the MIDI channel to "all"
- In your DAW, when you then select which MIDI channel you're going to record on, that keyboard should play only.
Hauptwerk is a disaster to learn, and the manuel is literally 700 pages long and incredibly complex. If you have any other questions, please ask. I'd like the time I've spent learning the info on this topic to be shared with others. 🍕