seasons all messed up

I cannot figure out what I’m doing wrong here. In the TV Shows section I am adding Star Trek TNG. I have tried to add all 7 seasons several different times several different ways and the results are always the same. All 7 seasons are grouped into 3 folders: One contains season 7, one contains seasons 1, 3 , 5 and 6 and the third one contains seasons 2 and 4. I’m naming them as follows.

STAR TREK TNG S01E01 NAME.AVI
STAR TREK TNG S01E02 NAME.AVI and so on

What am I doing wrong? Thanks for any help…-Curtis.

Plex is looking for it in the following format

/TV Shows <--- indicates a folder
   /Star Trek The Next Generation <--- indicates a folder
      /Season XX <--- indicates a folder
         /Star Trek The Next Generation - SXXEXX.ext

REF: https://support.plex.tv/hc/en-us/articles/200220687-Naming-Series-Season-Based-TV-Shows
REF: http://thetvdb.com/?tab=series&id=71470

This is the part that I’m confusing, could you please give me an example of how to name say season 1 episode 1?

I don;t mean to sound stupid but what is confusing me is the syntax. The / is what I don’t understand, where does it come into play?

I updated my original post as well.
I single episode would look like this

Star Trek The Next Generation - SXXEXX.ext

So, includind the TV Shows folder I would have three folders for each season?

Holy bat crap batman! You caused me to put 2 and 2 together and all I had to do was add a directory and all is good! I preciate the help very much…-Curtis