I did this on my home spinet organ. I got the organ last month used - it came from a church that was getting a new organ. I took some time fixing it up and it is now at least in some decent playing order. I recorded the organ part first, then using multitracking improvised the piano part on top of it.
I would have liked to record the organ directly with line in, but it didn't work so well. I ended up micing it, and it turned out pretty good with the additional benefit for turning the mono output into a stereo image. Those clicking noises you hear every so often in the recording is me switching stops - those tabs make a big click when you push them. The pickup of some of the bass notes at times was somewhat unbalanced (some were boomy, some were not as audible).
The addition of reverb was a bit tricky. I wanted to add it to give the organ more dimension. I used the church preset - the organ sounded great but the piano sounded like a tin can in a bathroom (there were very strong reflections). Removing reverb only from the piano part sounded very weird. What I ended up doing is applying the reverb separately to the organ and piano tracks. The organ track used the preset settings, and with the piano track I changed the mix of raw and reverb so there is much less reverb and more raw sound.
Improv - January 9, 2006 - Organ + Piano
Mic: (2x) Studio Projects B1
Interface: Edirol UA-25
Organ: GEM F-30
Piano: Yamaha C3
Enjoy!