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For smaller collections, you could organize and create the folders yourself. But for something like Ducks' collection, it's better done with Calibre.
As far as organizing with ADE, not really. Most people just use it to authorize their ebook devices so they can download and read DRM'ed PDFs and ePUBs. As far as I've seen, you can upload books using ADE, but it does not offer any folder creating options.
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