I've never heard anyone mention that mesalamines hurt the bacteria from fecal transplants. I believe I did read somewhere where someone said that steroid enemas might make it difficult for the bacteria to take hold, but I don't know if there's any truth to that or not. I've been doing fecal transplants and have done twelve so far. I'm also trying to squelch a flare, so I do Rowasa, steroid enemas, and fecal transplants once a day. I've never spent so much time on my left side! I have to center my medicine enemas around when my donor (my dad) "goes", so the time of day that I do the enemas vary. I think as long as you do it once a day at some point, you should be good. Good luck! You'll get used to the process after the first couple times.
I found this youtube video to be very helpful and straightforward with the how-to's. http://www.youtube.com/watch?v=xLIndT7fuGo