Make sure you're updated to the latest version in iTunes.
Open Reader and click Documents on the left.
TO MAKE A NEW FOLDER: Click Edit button (upper right). Click the New Folder icon (left icon). Name the folder.
TO MOVE A FILE INTO THE FOLDER. Click the Edit button (upper right). Click the PDF file you want to move (red check appears). Click the Move icon (middle icon), then confirm by clicking on the words that appear. Click on the name of the folder you want to move the file into.