These are some scripts I have to manage two versions of transmission that I run on my server. transmission.sh is the script I use with transmission's script-torrent-done. It gets the torrent, and copies all of its files to another hard drive, but leaves the original copies alone. It then calls my sickbeard post-processing script on the copy-directory, and the sickbeard post processing script does all the deleting it wants.
The second script I call now and then to move all the torrents from my sickbeard managed instance of transmission over to my normal instance of transmission. I didn't want to do this automatically as part of the script-torrent-done because sometimes I will set shows to sequential download (using the patch in another one of my gists) and watch them as they are downloading on XBMC. I wouldn't want those files to disappear while watching them! So instead I just call this script manually. Maybe I'll crontab it once a week or something, I don't know.