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You should probably forget about "structure", as your reader does not support folders.
The way to keep your books in order are collections. Collections are actually tags you attach to your books, as you might have seen on calibre. You can attach multiple tags, say "author", "series", and "read" to a book, and your book will appear in all these three categories. That doesn't mean that you have three copies of the book. You can't get around seeing ALL of your books under books in your reader. But you can browse by collections and see your books in a more ordered way.
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