[Adoby]

While the books are stored in calibre, you access them only via calibre. And then, as you say, you should ignore any filenames. Instead you use the userinterface of calibre to find, change, convert and examine books.

When/if you wish to access the actual book files you save them to disc, or send them to a device, and then you can specify exactly how you would like to use the metadata to name the files. Folders and filenames.

As theducks says, while in calibre don't think of the books as files. Think of them as books stored in a database.