Books are managed by the OS X application iBooks. You have to use iBooks in order to add books to your library. There is no Books section in your iTunes library where you can drag files to.
So just launch iBooks and drag files into the application window, and the books section in the synchronize tab will update immediately. Then, synchronize your device.
Also, if you try to add PDF files using File -> Add to Library, iTunes seems add those files as sound files, and they end up in the Music section of your Library, but won't be copied to your iOS device as PDF files.
Here is thread on discussions.apple.com, and the answer that pointed me to the right direction:
StumbleSally Midwest - US
Re: how to upload pdf to ipad
Mar 7, 2014 6:56 PM (in response to dawnrber)
With the recent update to iTunes (I'm now on iTunes 11.1.5), the previous directions for uploading an PDF and syncing it with iBooks didn't work for me because iBooks is now a separate program at least on Macs. Maybe iBooks has been separate for a while, but anyway, here's what I had to do:
- Start iBooks.
- Drag the PDF from my desktop to iBooks.
- Start iTunes.
- Plug in my iPad.
- Stop the auto-sync/back up process in the center window by pressing on the small "X" (yours may not be set to auto sync when plugged in).
- Select my iPad name in the left column.
- Select Books from the menu bar just under the iTunes center window (you can skip this step if you want to sync all of your books).
- Select the checkbox for the PDF(s) you want to sync (skip if you're syncing all books).
- Select the Sync button in the lower right.
- Once synced, go to iBooks on your iPad and in the Library, select Collections.
- Select PDFs.
You should now see all of the PDFs you synced.