You can get most of what you request using Plex’s current naming guidelines, which supports multiple episodes in a single file. That approach does have limitations. You’ll have better results splitting the files into individual episodes.
Also, Plex uses TheTVDB.com to match episode numbers and names. If you match what is listed at those sites, the episodes will appear correctly in Plex. You can use either the Aired Order or DVD Order, depending on how you want Specials to be listed. See the show listing for details on the differences between the two orders.
Separating files into individual episodes
SpongeBob SquarePants - s01e01 - Help Wanted.mkv
SpongeBob SquarePants - s01e02 - Reef Blower.mkv
SpongeBob SquarePants - s01e03 - Tea at the Treedome.mkv
Splitting files is straightforward using MKVToolNix, especially if you’ve chapter markers for each episode. See [HowTo]: splitting multi-episode files with MKVtoolnix GUI
Multiple episodes in a single file
SpongeBob SquarePants - s01e01-e03 - Help Wanted Reef Blower Tea at the Treedome.mkv
SpongeBob SquarePants - s01e04-e05 - Bubblestand Ripped Pants.mkv
etc.
There are limitations to using the multi-episode in a single file approach. It will definitely help to have chapter markers for each episode.
Plex Documentation
See Plex Docs -> Your Media -> TV Show Files (Naming & Organizing) -> Naming and Organizing Your TV Show Files for additional details.