Well I fixed my issue, mostly by fluke.
I moved all my video files to a different hard drive. I ended up deleting everything out of iTunes and then bringing it back in. I'm sure that wasn't the best way to have gone about things because all the editing of the video's "Get Info" that I had done went away. Needless to say I wasn't happy with the time I had wasted doing that. But it made me realize that fixing info in iTunes is a temporary fix. If I move files again or get another computer all that is lost. Why on earth iTunes doesn't edit metadata is beyond me, but I found a program that does.
MetaX for Windows. I believe the Mac version is quite popular.
Not only did it add the season and episode number to the video, but it also added the description, changed the show title, and even chapter titles. It also added the artwork that I wanted and much to my surprise when I brought the newly metadata'd videos into iTunes they played. No idea why that happened, but I am not complaining. Now my Apple TV looks much better.
Anyways I thought I would share my fix if anyone else has this problem and also to complain that iTunes is stupid for not editing metadata.