I had mine done right away during my first surgery and I believe, as Shaz said, that they did some parts of the procedure from the top and some from the bottom. Unfortunately, I don't really know the specifics of what the surgeon did to remove the anus... it does seem like a weird concept to remove a hole. Basically within my butt crack I now have a roughly three-inch long, ridge-like seam instead of a hole.... sort of like the skin was pinched together and then stapled. The ridge-like seam seems to allow it some "give" so that it doesn't feel tight or like my butt cheeks are sewn together:) It is really hard to explain. My surgeon did leave a bit of space between the staples for drainage, but I never had much come out of it compared to my stomach incision.
I was really surprised how little the butt incision hurt compared to everything else, even when all the staples were in. I thought it was going to be really painful to sit, but it wasn't too bad. It got a little itchy towards the end before the staples were removed, but nothing horrible. It still hurts a bit as it is not done healing, but I have had no problems with it at all so far.
Good luck and hope this resolves the problems you have had.
-Officially diagnosed with UC in 2006, though had symptoms since 1999.
-Had mild/moderate symptoms continuously until severe flare in autumn 2010 which required 2-week hospital stay
-Took Asacol, Rowasa, Canasa and Prednisone to manage flares but meds stopped working
-Tried 1 infusion of Remicade but had excruciating joint pain and discontinued
-Had permanent ileostomy surgery 11/8/2010