Can you remove PDF's after you add them to iBooks?
All the books that you move to iBooks stored in

~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/


iBooks make a copy of every books that you move on it.

With iCloud Sync the Documents are stored in the following location - Thanks to @Rogier

~/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents/


Personally I recommend that you make a backup or move your original ebooks on an external drive.