This is to explain the difference between the two folders.

The first, "Total Drama Equestria," is for any story that contains a setting similar to "Total Drama" but takes place in Equestria and doesn't include any "Total Drama" characters. The obvious example of this would be "Total Magic Pony Island".

The second, "Total Drama Teens in Equestria", is for any story where one or more characters from "Total Drama" end up in Equestria. They can be either ponyfied or remain human.

Hopefully that'll clear up any confusion you might have.