Calibre has to store copies of all your ebooks in it's own directory structure. You can't change this structure. Your original ebooks are still where they are in your original directories. Calibre does data manipulation on its own copies.
If you don't want to read Calibre's copies with Calibre, after you convert or edit a book in Calibre, do a "Save to Disk" and save it where you want it in your old, original library folders. Then read your books from your original folders. Or, do a "Send to Device", and the file with the updated tags and such will appear correctly on your reading device.
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