Changing the Calibre File Structure
The simple version:
You can't. Not yours.
The detailed version:
You are probably accustomed to storing your metadata in your computer's filesystem. That is, you are using the names of the folders to keep track of information about your books. That's how we all started. Calibre is why we stopped.
For example, you might have a folder called /ebooks, and under that you have /ebooks/nonfiction, /ebooks/fiction, etc. One of those, in turn, might have /ebooks/fiction/fantasy, and under that /ebooks/fiction/fantasy/lackey. The name of the folder gives you the type, genre, and author. So far, so good ... if you want all your Mercedes Lackey fantasy novels, you can find them right there. And you've probably got a folder called /ebooks/fiction/fantasy/flint where Eric Flint's books are stored.
But where do you put Shadow of the Lion? Under /lackey, /flint, or /freer? How about a book that has both fantasy and SF short stories? Where does a SF mystery, a historical fantasy, or a near-future thriller go? And that's just fiction. Non-fiction gets even hairier. Filesystems are actually a pretty crappy way to store metadata.
That's where calibre comes in. Calibre stores metadata as metadata, as much of it as you want. You can tag Shadow of the Lion as fiction, fantasy, historical fiction, and to-be-read, if you like, and it will come up in the list when you select any or all of those. It can be listed simultaneously under Lackey, Flint, and Freer. You can also note that you got it from Baen. And none of this has anything to do with the filesystem.
Calibre organizes books. Calibre is not a file organization program. Calibre is a book organization program. It's more than just the card catalog to your library -- it's the librarian who goes back to the stacks and brings you the book you're looking for.
The reason calibre copies all those ebooks over into its own set of folders is so that it can have exclusive access to them, and so it can know exactly what they are, where they are, and what they're named. Think of it as a black box, one with a big warning label stating "NO USER SERVICEABLE PARTS INSIDE!" Or maybe a storage room with a locked door with a sign on it saying "PRIVATE - Calibre Only".
You don't need to find those files with your computer's file manager. Calibre is there to do that for you -- or, rather, calibre is there to find your books for you. It will display your books, put them on your ebook reader, whatever you need, without you having to care about the actual computer files, only the books. If you actually do need one or more files -- perhaps you want to pack up all of the Harvard Classics to give to a friend -- calibre can collect them from its black box and put them wherever you want them -- and in whatever format you need to have them in.
The transition can be a bit hard. You're used to thinking of your ebooks as files and your filesystem as their metadata. Using calibre means thinking of them as books, abstracted from their computer representation, and with much more comprehensive metadata. It's a different way of looking at them, yes. But once you've made the jump, you won't want to go back.
You see, I started out the same way you did. I had all my neat hierarchical folders, my metadata in the filesystem, and I liked it that way. Then I found calibre. It took me a while to get my head around the whole idea of dealing with books instead of files, but once I did, I've never gone back. And now I'm explaining it to people who are where I was a few months ago. Give calibre a try, and you may end up doing the same!