Apps section in iTunes...is there an app like Goodreader where you can create folders

[Matth3w]

So I use my iPad mainly for work. I have about 600-1000 PDF documents I want to organize. I've been using Goodreader for years. The issue is the initial sync of the Folders, it's too clunky. I have to drag a million files into the Apps section of iTunes, and even if I have the folders already created and showing up in the little drag to box, I can't actually put files in that way through iTunes.

Is there a better app or a better way to do this?