After looking everywhere in the Custom Story section the only thing that came close to solving my problem was the installer stickied. That didn't help one bit because it doesn't explain where to put your files or anything. So yeah please help.
Normally, after you download the custom story and unpackage the file, you just place that folder into:
If you bought the game else where, by default:
C:\Program Files\Amnesia - The Dark Descent\redist\custom_stories
Or if you bought it off steam
C:\Program Files\Steam\steamapps\common\amnesia the dark descent\custom_stories