I am taking Flagyl and Cipro together, twice a day. I sometimes get a stomachache from it, but I make sure to take it with food, and this cuts down on the stomachaches. It really helps me with fissures/fistulae. If they are getting to the point where I'm almost too sore and raw to wipe, I take the medicine and within a few days I am not as senseitive down there.
I also eat Activia once per day while taking Flagyl. I figure that it repopulates my instestines with good bacteria, but for all I know it my be a waste of money because maybe the drug kills the probiotics as well...