[Grauheim]

I've noticed considerable confusion about how Calibre works. Much of this comes from an important Calibre feature that a lot of people fail to realize exists.

As others have said above, you should ignore how Calibre represents your books internally. Treat it like a black box.

If you want to also have your files available in a directory structure outside Calibre, the way to do it is (1) first enter your books into Calibre, and then (2) use Calibre's "Save to Disk" command to save them to your own file hierarchy.

Now here's the trick that a lot of people miss: in the Preferences|Add/Save|Saving Books dialogue, you can specify exactly how books are saved. For example, I put mine in a folder structure of Subject area (e.g., history, science fiction)->Author name (last name, first name)->book title. Calibre gathers this information from the meta-data and automatically puts the book in the right place. This is much easier than trying to fight Calibre by manually maintaining your own folder structure on the side.

I personally keep all my books in Calibre, and use the Save to Disk feature to transfer them to my Opus in a folder structure useful for that device.

While nothing's perfect, over all, Calibre is an immensely well designed system with a lot of rich customizability allowing you to tailor it to your needs.