1. Make sure to have the files properly titled. IE: Aqua Teen Hunger Force - S01E01 - Rabbot.avi
2. Have a folder for each season, and all episodes within that folder (May not need to be. But it worked for me).
Now, after making sure all files are neat and pretty, go to boxee and go to: Menu > files > source/directory (where files are located) > select file folder > select season > select first episode > go to left and select 'identify' > select 'search' > select the proper TV series > confirm that the season & episode are correct (01 & 01), and then CHECK MARK "Try to apply season details to all files in folder". Then select 'done'.
Boxee will then go from file to file within that folder, and get info for each episode. Once done, do the same thing for the next season folder, and then the next season, and so on, and so on.
I hope this is what you were needing. I had gone through this myself 2 days ago, and this is how I was able to fix all my '1969' TV shows listing just one poster, and a TON of files rather than broken down.
Good luck bud!