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I have to assume you have a local version of your library. I for one would never want to trust the only version of my important files to dropbox without a good backup.
I would strongly suggest that you use your local version of the library (the calibre folder structure with the program's naming etc) to perform all the maintenance. The tagging, marking as read etc.
When all is as you wish you can then use your "Save to disk" option to save the files (books) to the dropbox location you want. Using the Preferences -- Saving books to disk you will have the option to set the template for how to name the files.
For instance, you can setup a custom field for the main subject matter of your books. eg subjectshow. So if the subjectshow is topicA and another subject show is topicB you can have the save template setup to save the books by main subjectshow. and use author_sort to list the authors by lastname, firstname.
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