How do I use Automator to add files download via Transmission to iTunes?
A couple of solutions come to mind. 


Have your Automator script move the files to the trash (or another folder on dropbox, like "Added to iTunes") after it copies them to the Automatically added folder.  
Set your automator script to check your dropbox for files every x minutes (e.g., 15). Tell it to only copy the files that were added in the last x - 1 minutes (e.g., 14, or 14:59). The Spotlight metadata element you want is kMDItemDateAdded.   
Far and away the easiest solution is to use Hazel.