Use one folder per show and season folders inside it. Include season and episode numbers in every episode filename.

TV Shows/
  Example Show (2024)/
    Season 01/
      Example Show - S01E01 - Pilot.mkv
      Example Show - S01E02 - Second Episode.mkv

Use S00 for specials when the metadata source treats them as a specials season. Keep multi-episode files and alternate cuts consistently named so they do not appear as duplicates.

After changing episode names, scan the library and confirm that episodes appear under the correct show and season.