When I got my Story it came with 100 free books. I had the top level folders you have named, like Books, Comics, etc, and under Books was a folder English Books containing the 100 free ones. I immediately created subfolders, one for each author, and moved the books into these subfolders. Some authors only had one, others, like Shakespeare and Jane Austen, had loads.
One advantage of this was that I could rename the books. I had a book by Chekhov the name of which I still don't know, since the book file is called "Anton Pavlovich Chekhov - Some book title" and only the first three words can be seen on the screen! I have discovered, btw, that you can call a book file "Author - Title" or just "Title" and the Story will allow you to create a Bookmark. But if the book file is called "Title - Author" you can't create a Bookmark. This option is just not available on the Options menu.
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