Mine goes into the j-pouch above the cuff. IMO that is where it is supposed to be. The medication will mix with excrement but there is no avoiding that. I try to insert it after I've emptied my pouch to make it most effective and lay down after insertion. During bad times of 15 BM's a day, for example, it's impossible to wait for an empty pouch. These are also the times when we need canasa the most. I insert it, lay down and hope for the best.
I also use Anucort, hydrocortisone suppositories if everything is too inflamed &/or painful. This is to bring inflammation down so the expensive canasa will be more effective. My GI's instructions are to use both kinds of suppositories like this. Some get results just using anucort.
When I was first diagnosed I didn't have good results with either kind of suppository. My local GI referred me to the Mayo CLinic. The GI there told me to keep using the canasa until the cuffitis went away and it took months. I was first diagnosed locally in January and didn't get to Mayo until May. I think it was at least August when I felt it was totally gone. Subsequently I've had to use it at least 2 times a week to keep the symptoms away. I am not the normal person as I have it chronically. I hope once yours clears up that you can stop using the suppositories.