Hello Scott,
If you don't already have it, the sample set developer documentation is available upon request to licensed Hauptwerk users -- please send an email to support[at]hauptwerk.zendesk.com if needed, mentioning that you'd like a copy.
That documentation covers the organ definition file (ODF) format, in concert with the "Design tools | View organ definition format documentation" menu option in Hauptwerk (which is available once the relevant licence is activated).
Aside from providing the documentation, we don't officially provide support for editing 'full-format' ODFs, but briefly you would need to add new CombinationElement records for each of the desired CombinationIDs, respecifying your new SwitchID for CombinationElement.ControlledSwitchID and CombinationElement.CapturedSwitchID.