I just went to my check-up last week. I never had a 3 month check back because it was a long drive and I was having no problems (we did it over the phone). I had my take-down in April of 2011 and wanted to wait until summer break to get it done.
They went over my history with me, did a manual exam then gave me 2 fleet enemas and did an internal exam. I didn't know I was going to have this exam and did not prep, but she said that was what the enemas were for. I inserted those, held it for 5 minutes, then emptied. She then did the scope exam. It was uncomfortable, but not horrible. I guess I have irritable pouch syndrome, so that didn't help matters. She took a lot of biopsies, so that hurt a little and hurt for several days after as well as cramping. Not too much bleeding.
She said that everything looked beautiful and if the biopsies came back normal I wouldn't have to come back for 2 years.
Since I was feeling good and the drive to the Cleveland Clinic was so far, I had contemplated not going back. I am glad I did. Every time sometime new would happen I wondered if something was wrong with my pouch. It was reassuring to hear that everything looked good.
So, a long answer and much more information than you asked for, but I hope this helps. Make your appointment and then ask your surgeon what your check-back schedule should be going forward.