New guy having basic issues...

So I'm using Transparency at the moment.
It seems like it took all my movies and added them into one folder.
And got rid of my TV shows in lieu of some random junk shows.
I have no idea what's going on.

I have my files set up in a very basic way.
Each folder: Movies, Television, etc. contains folders A-Z.
How do I simply point the Movies link to the movies folder and show the A-Z folders?

Thanks.