Put the show name in the episode file name (Plex naming convention). Also, part1, not part 1 (no space) as mentioned by Juice.
Modify the file names for all episodes in season 6.
/House/Season 06/House - s06e01 - part1.mkv
/House/Season 06/House - s06e01 - part2.mkv
After changing the names, Plex Dance the entire season.
Edit: As mentioned in the documentation, not all Plex clients support multi-file episodes. In the long run you’ll be better off combining the parts into one file. The process is very easy and very quick with MKVToolNix. No transcoding is performed. The two files are simply combined into one file.
