I'd put it in the loop. If you want to play a clean rythym then dirty wank over top you have to have it after your dirt. At the front changing pedals changes the repeated sound. In the loop it loops only how it sounds when recording.
No problem at all using it in front as long as your amp is clean. I always use mine in the loop of my Mark IV though because I frequently use the dirt channels...however, I do find that my saved loops can sound a bit muddier in the loop than in front.
Update: So, I tried it both in front and in the loop. When in front, I experienced a little tone suckage. What bothered me more was the volume loss. My rhythm loop would be playing and when I would start to so over it, the volume would drop significantly of the rhythm loop. I then put the RC-3 in the effects loop and didn't experience any tone or volume issues. In the loop it stays.