iTunes\TV Shows\Show Name\Season S\S-EE Episode Name (if HD)
The files are stored as .mp4 or .m4v, and have all been tagged with a program called iDentify. This program works flawlessly on the Mac and provides all the right information to iTunes. No mater how I setup the file naming structure iTunes renames it as listed when managing the shows.
Please let me know how I can get these shows to identify without manually going through each of the hundreds of shows that are currently unidentified.