OK so maybe that's my problem. I have everything that's done, dumped to F:\Documents\Done\. There are two folders (Movies, TV Shows) along with all the downloaded folders. Ill try your method.

This is my settings.bat right now: ::Update only what comes after the equal signs ::Escape any special characters [i.e. ()|] by inserting a carrot ^ in front, so for example (Movies) becomes ^(Movies^) ::Do not use quotations marks "" ::set uCompletedDownloads to the folder uTorrent is set...

I can not for the life of me get this to work.
This is what I have for Run this Program:
“F:\Documents\Ufiler\uFiler.exe” “F:\Documents\Ufiler” “%L” “%S” “%P” “%N” “%D” “%K”
Every time a download finishes, it just moves the file to: F:\Documents\Done
Am I missing something?