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Are you talking about calibre's own library structure, or about where books go when you export ("save to disc") them?
If it's the former, ignore how it's set up. Pretend it doesn't exist. Put a tent over it and forget that it was ever there. Paint it pink and set up a Somebody Else's Problem Field. In short ... don't mess with it.
Calibre doesn't exist to organize files; it exists to organize books. What files they're in, and where, doesn't matter. If you need to do something with the actual file, then export it from calibre to wherever you want.
A lot of people are accustomed to using their computer's filesystem to store metadata. That is, you might have a book stored as \fiction\mystery\doyle\baskervilles.epub. And that works, kind of ... but what if you want to zip up all of Arthur Conan Doyle's books, even the ones that aren't mysteries, and send them to a friend? Or what if you want to do something with all your Sherlock Holmes stories, even the fanfic your friend Joe write that you have filed under \fiction\mystery\fanfic\joe1.epub, etc? You'd have to go rummaging around in an awful lot of folders to find the right ones. Or what if you have a book with two authors -- which one does it get filed under? If it's written by Smith and Jones, if you file it under Jones, you'll miss it when you're looking for all of Smith's books, and vise versa. Computer filesystems really aren't very good for storing book metadata.
With calibre, the database manages metadata -- that's kind of the whole point. It doesn't matter where any given file is; if you want all your Doyle books, you just select the author name and there they are, ready to do anything you want with them. The way I have my tags set up, for instance, I can search for all the SF written by David Drake but without Eric Flint as co-author, or all the David Weber novels that aren't military SF (he did write a few!).
That's what calibre is for.
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