Moryoav, you assume that uTorrent is supposed to move the files for you when you do that, don't you? Well it doesn't. Stop the torrent Move the files Set the download location Force a re-check to verify the set download location worked right Start the torrent
If you know for a 100% fact that they don't share peer information, keep them separate. OpenOffice and Slackware both run the same tracker package in a similar configuration. Do NOT separate theirs. And as a general rule as a downloader: DON'T FUCK AROUND WITH IT!
Openoffice torrents run on a linked tracker cluster. I know this because I helped set it up. Announcing to all the trackers is a complete and utter waste of resources for both you as a downloader and us as tracker administrators. And no, different domains is NOT the deciding factor for wether or not trackers need to be in separate tiers.