Creating/using folders in iTunes apps section for sync (not iOS folders)

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?

Making folders in iBooks :
http://m.youtube.com/watch?v=5NCTpGAik8M
Emailing the iBooks :
https://discussions.apple.com/thread/4459938?tstart=0
Its fine if you dont want to use Sir.
But you have the options in iBooks :)

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