When you first start PDF Bookshelf, it will ask where you want to store your bookshelf. If you already have a bookshelf and want to replace it or create another one (PDF Bookshelf only supports having two bookshelves open at one time, but you can have as many bookshelves as you want), choose Bookshelf > New.

Your bookshelf is a package, a special directory that your Mac will show you and allow you to access as if it was a single file. Inside it, PDF Bookshelf will store and index all the metadata for your imported PDF files and, if you so desire, those files themselves. When creating your bookshelf, you can select where to create it on your Mac and whether to store your PDF files inside the bookshelf package or in an external folder of your choice. You can also tell PDF Bookshelf not to copy your files and just remember where they are. However, if you do so, PDF Bookshelf will not be able to automatically update its data when you make any changes to these files.

Note that deleting a bookshelf package you will also delete any files stored inside it.