Each stop should be set as a different instrument but set to the same channel. At least, that's how I do it.

How do you then change them mid-score when a change of registration is warranted.

I takes a bit of fiddling, but what i usually do is create separate files: 1) a reading score; and 2) an audio score. For the audio score, I setup a staff for each manual or registration change. I haven't done it in a while so my memory is not 100% on the specifics.

George, thanks for the advice.  It is extremely helpful and seems logical.  I hope they come up with an easier way of doing this in the near future.

I second Columbus's request.  I was very disappointed that Garritan organs does not work at all like a real organ -- i.e. stops added or taken out.  Rather, every combination had to be pre-mixed and saved to a different channel; a lot of work to replicate a simple on/off.  At the time I wrote with suggestions on how to implement -- no response.  George's workaround is another solution, but also much extra work.  

Here's the workaround I've used, which you may find helpful.  First I save the finished piece as a midi file and open in a sequencer (e.g. Performer).  This gives me much more control over playback than is possible via Finale and Aria Player anyway -- yes, more fiddling, but worth it for natural, predictable playback. Then I make a copy of each manual's track for each stop I want to use, e.g. one for the 8' principal, one for the 4' flute, etc.  Each stop gets its own channel.  (You can have a stop played by any manual this way, but if you want a different sound, e.g. a Rohrflöte on Swell and a Gedackt on Great -- or different panning -- then you must use separate channels.)  Then I add track mute control changes when I do not want the stop to sound.  (This seems better than copying and pasting notes because it's simple to revise later when a stop goes on or off.)  So if you have three manuals and pedal, this gives you four stops for each within sixteen midi channels.  I've also used many free Hauptwerk stops, which seem to be easier to access and tweak and better sounding.  Although not simple, it's more intuitive and easier to control.  Has worked for me and might for you.  Much as I hope Garritan will update the organ engine one day to make it more like a real organ's controls, I'm not holding my breath.