I’m no expert, but I’ll take a stab at your issue. I have also attached a 2TB external drive to my ATV and setup as primary. As I understand it, if you have iTunes compatible content (while it is not required), the best way to manage it is through iTunes itself. Drag the movies to iTunes, then sych w/ATV. That should solve your issue.
BTW, I did discover that if I drag movies (in my case ripped DVDs) to the “movies” folder (which defaults to the user FRONTROW), after making my external disk primary. The movies show up on the INTERNAL drive, and do not go to the external drive at all. What I did to solve that problem is: a) Created a new “movies” folder here: sftp://appletv.local//mnt/Scratch/Volumes/MediaHD (I also creates some sub-folders to organize my stuff into categories (Ex: DVD, Documentaries, Concerts, etc.). b) copied the content that I had already SFTP’d to the new folders c)deleted the movies from the (default) movies folder d) Then I created symbolic links in the ATV movies folder (on the internal HD) which point to these folders on the external (ex: short cuts or aliases). I did not know how to tell nitoTV to go to these folder, so the symbolic link idea was the only option I could think of. Anyway that works like a charm. Some basic UNIX skills were needed to get this done (via mac terminal).