[Adoby]

You start by adding your books to calibre. Make sure that metadata is uniform. Always the exact same spelling for each author. Fix series information and covers and so on. Add tags to help finding books.

The books will be stored in the calibre library and can be efficiently accessed from the GUI. You can create virtual libraries for genres and rate the books and a lot more.

You can then save copies of the books to disk, and then rename the files, using metadata fields, as you please using the save template. Either both using folders and filenames or only using filenames.

In a similar way you can send copies of the books to a reading device.

What you can't do is change how the books are stored and named in the calibre library. If you try calibre will loose track of the books and you can no longer access them from the GUI. The books stored in the calibre library are NOT intended to be accessed directly from file managers, only from the GUI. This often cause great confusion and frustration for new users not used to using the calibre GUI to access books.

If you only intend to access the books as the new renamed files, then you can delete them from calibre after you saved copies of them to disk. But it may be a good idea to keep them in the calibre library so you can make sure that you don't add duplicates and so on.

If you experiment a bit you may even find that you don't want to rename and save the books to disk at all, it is much easier to access the books in the calibre library directly from the GUI.