I unchecked the box "Copy items to the iPhoto library", because I don't want iPhoto to duplicate my photos, but it still copies them. What could be the problem? I want to use my organized photo library as a referenced library in iPhoto.
I would go for the "Copy items to the iPhoto library" option as this will prevent problems in the future when you have unwittingly/mistakenly deleted the originals, or you don't have the external device that they were on to hand.