I'm another one that uses Calibre. I want a record of all my books in one place. That way, I won't buy an ebook if I already own the audio or vice versa unless I do it intentionally. I keep records of every library book in Calibre too. The ability to enter data in Calibre without an ebook is wonderful.
For the actual audio files, I have then all in one directory that is kept backed up. I can find a book I want to listen to in Calibre. Then I just go to the directory with all the books and find the folder or zip file within the main directory by name. Very easy and works well for me. YMMV
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