Hello Philip,
[Topic moved here. Also in answer to your email to us on this, in which you also mention that the problem is within Reaper, not within Hauptwerk's settings:]
Reaper's makers make changes to Reaper's user interface very frequently, so it's very possible that there have been some relevant changes since our tutorial was written. Beyond providing the (albeit probably now rather out-dated) tutorial, we can't provide official help with using Reaper itself, I'm afraid, but if Reaper's documentation doesn't help then you could potentially try contacting Reaper's makers for support, or perhaps some other Hauptwerk/Reaper users here will have some suggestions.
The Hauptwerk plug-in just provides 16 stereo outputs, and the settings within your Reaper project would define where they're routed.
I recall this similar topic from last year, which might perhaps also be useful: viewtopic.php?f=3&t=14082