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A couple of options:

1) (what I do) You can stack the files.  Go into the movie database editor tab, delete all but one of the records for a series.  Then edit the remaining one and add multiple video files to it.  Personally, I keep one record for each season, and stack the files by season.

2) Check out the My TVSeries plugin.  Handle episodes and seasons is exactly what this plugin is designed to do.

Link here