* yes, either use a normal MIDI cable to a soundcard, or an USB-MIDI cable directly to the computer, and run the normal Hauptwerk procedure to detect MIDI devices
* yes, connect the audio outputs on your external soundcard to the aux input of the organ (if present) using the appropriate audio cables and connectors
* yes, if the stop knobs generate MIDI signals. A simple hack to silence the organs own sound is to insert a headphone plug, but perhaps this is not useful if you want to use the internal speakers.
Please let us know the exact model if you need more specific info.