iTunes Workflow - Duplicates

I have files stored on two externals. I'm trying to find the right workflow for backing up all of the files from External 1 on to External 2, leaving whatever isn''t duplicated on External 2 alone (some of the files are already there but not all) and then having iTunes index the entirety of External 2. I'm trying to avoid having duplicates on External 2 so that when I finally go into iTunes Prefs and point to the main folder on External 2 where the music is I don't end up with duplicates in iTunes. Any suggestions?

I answered this in email already but look into using the sync action to sync the whole folder from one drive to the other.