Gosh, at the risk of sounding like some kind of expert, which I am clearly not, I'll give you my 2 cents worth. So much depends on your sample set, but for the sake of argument lets assume you have a 2 manual plus pedal classical organ with about 30 - 60 stops.
Here is just a suggestion of a place to start, with additional tweeking later after you have had a chance to hear it.
CHANNELS
All 16' & 8' pedal ......... | 1 ............... 2
including reeds, and .... | (with subwoofer)
midi notes 36-48 of ..... | Panned Stereo
16' manual stops
Both manuals ............ | 3 .......................... 4
reeds and strings ...... | C,D,E,F#,G#,A# ... C#,D#,F,G,A,B
all mixtures ............... | Cycled octaves
4' pedal stops
Both manuals ............ | 5............ 6........... 7.............. 8
principles, flutes ........ | C,C#,D... D#,E,F... F#,G,G#... A,A#,B
8,4,2,1 ...................... | Cycled octaves
This setup would require an 8 channel audio card such as the EMU 1820, 8 Behringer Truth Active monitors and 1 Behringer Active subwoofer plus 10 1/4" TRS to XLR patch cables
All for about $2000 from
www.americanmusical.com
Well that's my story and I'm sticking to it. Until tomorrow :)