Create categories with iBooks (Mavericks)
Go to: ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books and make a backup copy the file Books.plist. 

Double-click Books.plist when it should open in Property List Editor, assuming you have Xcode installed.

Expand Root>Books and examine any item from Apple to see the format. Find the item containing your PDF (I'll call it 'itemX') and open it. If there is genre key all you have to do is edit the value field. If not, select 'itemX' and click on 'Add Child' at the top left to insert a new blank key/value pair.

Fill in 'genre' for the Key, String (the default) is correct for the Type, and for the Value insert the category you wish to associate with the PDF (you can invent your own).

Save, restart your computer, open iBooks, and your PDF should now have the category you assigned it.

Next you have to sync your iPad to your Mac with iTunes, but before you do that you need to delete the PDF files from your iPad, so that you have the 'new' versions with the changed categories. You may have to restart your iPad to see the changes.

A bit of a faffle, but it works for me on Mavericks with my iPhone.