XBMC and iTunes Naming Conventions

So I recently got an Apple TV3, and I was very happy to set it up. I bought a copy of iFlicks and I put all of the files that I have been using on my other media center into iTunes. Now, for me it does not make sense to have two copies of every file, and I cannot seem to figure this out. I would like to have XBMC run off of the iTunes Media folder, but when I point the scraper for TV shows there, none of the episodes show up. However, all of the TV show names pop up.

Can anyone help me with this, as I would really not like to have two duplicates of all my media.

Thanks,
Macmac13