The way that I did it was I downloaded a TV show from iTunes and I "right" clicked on it and clicked "get info". I then saw what info they had in theirs and copied that in the ones that I handbraked. For example, where they had the TV series name I put the TV series name. Where they put the season number and episode number I put that info. You can go so far as to put in the descriptions and everything.
The big thing for TV shows is to go to the options tab and set the Media Type to the correct type (Movie, TV Show or Music Video). If you don't do that everything will default to Movie and will show up in your movie section.
Hope this helps. If you have any specific questions feel free to ask. If you have a lot of media it can take some work getting it all done. But in the end it is worth it if you care about everything being organized.
-JC-