@emellaich, thanks for the thoughtful and helpful reply! Naturally, your answers give birth to more questions.
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I'm not sure what you mean in terms of compatibility. You need to be aware that Calibre creates its own directory structure in order to manage the books it catalogs.
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Meaning, it creates its own directory structure within the desktop library? Does that have any effect on the directory structure within the Sony Reader?
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It first creates folders for each author. Then within the author folder it creates a folder for each book title. When you 'add' a book to Calibre it leaves the original book where it is and then creates a new copy and places it in the proper Calibre folder hierarchy.
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When you say "it leaves the original book where it is", I am assuming you mean "where it is" on the computer? It does not alter the location of the original file on the PC? Yes?
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Now, there is nothing special about these folders.
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Meaning, the Calibre folders?
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Using Windows you can browse to the folders on your computer and see the documents with no problem.
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Meaning, Calibre's folder hierarchy is not packaged in an internally managed binary - it can be accessed on the computer, making use of the standard Windows (or Mac) folder structure?
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However, this means that you can't read the same physical book collection from two different library software programs.
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Meaning, Calibre's library must be "read" with Calibre, separately from the Sony library or the Adobe Digital Edition's Library? Each maintains and addresses such libraries separate from the other.
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Each program would catalog their own set of books. If you need to share a book, then Calibre would copy it from the original place into its directory structure. Furthermore, any changes that affect the physical file would need to occur in two places.
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Meaning, that each library has its own copy of the book? Yes?
To clarify, I will not be maintaining the same books in differing libraries. I will have a set of books from Sony, a set of books from ADE, and a set of books from Calibre (acquired from Fictionwise and other sources requiring a conversion). My primary concern is the effect (or lack of same) to the Reader.
Your info is very helpful - however, I am not certain yet as to the effect of all of these different libraries to the Reader - I assume the Reader will "handle" it all?
Thanks for all of your time and trouble!

-- Rique
[edited a typo - RS]