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As eschwartz said, withing the Calibre Library Manager you have no control of the file and folder naming.
If you "export" a book from the Library using the Save to Disk function you can control, via Preferences, how the exported file is named and you can control into which folder (outside of the Library) the exported file goes. This ability of Save to Disk works the same whether it is dealing with the result of a Calibre conversion or with the original book imported into Calibre. Save to Disk does not alter the file and folder naming of the books within the Library.
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