Creating custom library not adding all files

Okay!! I know exactly what you want!! You will need to do what I suggested above. ITEM 2.
2. Double up the folder structure the series is in

Game of Thrones (2011) <-- Say this is ROOT
  Game of Thrones (2011) <- Plex will see this and try to match a series called Game of Thrones that was released in 2011.
    Season 01
    Season 02
    Season 03

I use this method for family/friends with kids. Their kids get the “kid section” of my library but every so often the parent wants their kids to have something from the “adult” sections.

Take a look at this post.