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With the 300 you can not organize the books from the reader. You have something called collections, and they are grouped by "tags". In Calibre (I don't use Sony's software) you can edit the books and create different tags for the books - Classics, Thriller, NonFiction etc... Then when you start the reader you can view your collection by Title, Author or Collection. I believe the 600 is the same way.
As far as Adobe or Calibre having the books, the reader makes no differentiation at all. It doesn't care how the books got there and they all appear together.
Hope this helps.
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