I'm not sure if you are expecting to hear Hauptwerk sounds from the Allen's sound system or Allen sounds.
HW will not sound through Allen if your computer's audio output is not connected to the Allen organ. Allen's are not delivered with audio inputs. They requires a separate interface box that is generally installed by an Allen dealer. To reduce hum and noise, you would also want to add an audio interface for your computer that provides balanced audio outputs. There are many threads on this forum that discuss audio interfaces.
If Allen sounds are not heard, verify that Allen's "Organ Local Off" setting is disabled.
The below paragraph is from the Allen Quantum manual:
9. Organ Local Off
Organ Local Off is a function that allows the user to “virtually” disconnect the organ’s
keyboards, pedalboard and pistons from the tone generation and capture system. In essence,
the organ is transformed into a multi-manual MIDI controller. To enable/disable the Organ
Local Off function, advance to the ‘ORGAN LOCAL OFF’ window function (see Section A2).
Use the "▲" and "▼" buttons in the Console Controller to enable/disable the Organ Local
Off function. Note: When Organ Local Off is enabled, the MIDI stops do not need to be on
to play the external MIDI device(s).