I love Boxee.  I have a vast collection of dvds that I ripped to iso’s and just recently began ripping my television series collection (Highlander, Twin Peaks, Buffy, Fringe, etc).  My biggest frustration in this process is that Boxee doesn’t provide an easy way (yet) for multiple episodes to be recognized from one dvd.

The answer is symbolic links. If you create a symbolic link for each season and point it to the iso file that contains that episode Boxee recognizes the episodes and adds them to your database.
The format is as follows:

ln -s path_to_iso name_of_episode

ln -s /tvshows/”24 Season 1 Disc 1.iso” “24.S01.E01.iso”
ln -s /tvshows/”24 Season 1 Disc 1.iso” “24.S01.E02.iso”
ln -s /tvshows/”24 Season 1 Disc 1.iso” “24.S01.E03.iso”
ln -s /tvshows/”24 Season 1 Disc 1.iso” “24.S01.E04.iso”

Obviously, you do this from command line.  If you don’t want to mess with pathways, just navigate to the folder where you keep your iso’s and have at it!    Hope this helps.