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Ok, everyone behave themselves or I'm turning this forum around and we're going back home!
All seriousness aside, one of the hardest things for most new users to calibre to understand is calibre does NOT organize your books in the folder/filename tree structure we are all used to. It uses meta data (tags) to allow more flexible and complex organization. When you first add a book to calibre, it copies your book to its own folder (referred to as a library); your original file is untouched. This library is for calibre's use only. When you want to access your book, you do so from within calibre. If you want to look at the contents of a book, you use calibre to open it. If you want to put a book in a device, such as an e-book reader or a card, calibre will do it for you. Calibre is not a mere database; it is a book management program.
I can understand a new user's paranoia about allowing calibre to take complete charge of your books. What if you decide down the road that another program better meets your needs? The way calibre stores books would make it difficult to access your books if you went directly to its library. However, by using calibre's Save to Disk feature, you can put your books into a folder (or multiple folders) using whatever filename structure you specify. Or you can do like I am and just keep your original files in your own for "just in case" (remember, calibre doesn't do anything to the original file, it just copies it for its own use). I know I don't need to but with old age comes paranoia. Besides, I still have lots of disk space.
Because it is so tempting to go poking around inside calibre's folders, once I create a library, I hide the folder so it can't be seen. That keeps me or anyone else from accidentally (or otherwise) mucking about in there (out of sight, out of mind). Calibre is still able to find it just fine.
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