Hello Doug,
The 'Performance tuning: Setting the audio output level' section in the main Hauptwerk user guide (pages 212-213 in the current v4.2.1 version) covers how to set levels optimally within Hauptwerk itself. In particular, you should set the 'Trim dB' setting on Hauptwerk's 'Audio, MIDI and Performance' large control panel ('View | Large floating control panels ...' from the menu) so that Hauptwerk's audio level meter occasionally *just* goes into the yellow, but never into the red, when playing the current organ (e.g. St. Anne's) in Hauptwerk on 'full organ' (with the largest registration that you expect to use with it).
Here are some other previous forum topics that cover setting audio levels (both with Hauptwerk, and on the computer's audio interface and amplifiers and speakers) in more detail:
viewtopic.php?f=4&t=13819#p102235
viewtopic.php?f=17&t=16198