iBooks files duplicated?

I have been putting some downloaded magazine PDFs into iBooks as it's simpler to access them from there than from the Finder. However, doing this, it seems as though I am duplicating the files - ie the file is present where I stored it in the first place and then when I put them into iBooks, the file gets dropped into the iBooks folder in ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books.

Is this correct? Is there a better way of doing what I am doing?