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if you are talking about the Sony ReaderLibrary application, you can move your books from the file where they are stored on your computer to Calibre. NOT using the actual Sony application. On my computer (I have Windows 7) the Reader Library files are stored in Computer > Documents > My Books > Reader Library. From there, drag and drop into Calibre. Bear in mind that most stuff if not all that you get from Sony is DRM-infested and you will be able to use Calibre to store and transfer books to your reader, but you will not be able to read them in Calibre.
ReaderLibrary does download books directly and only to the Reader Library folder with no other options, so yes that is how it is supposed to work. If you uninstall ReaderLibrary you won't be able to download books from Sony.
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