Editing file directory

I’m trying to upload some very complicated javascript I downloaded to the wordpress site I am helping a friend with, and in order for it to work well, and it is designed to work in a particular file structure. I’m finding it is difficult to change the file structure of the site automatically, and making it so that web designers can easily change the file structure from the menu would be very useful.

I have been using wordpress for two years now for the other site I am working on and this is the first issue I have had, I love this program!