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You have two choices: Keep your files in your own structure, or use the library management features of Calibre. These two are incompatible with each other.
If you really insist on keeping your files where they are, you can still use other parts of Calibre. For instance, you can use it for conversion (import into Calibre, convert, export from Calibre, delete book from Calibre). You can also use Calibre's reader for your books (associate ebook file types with ebook-viewer). It's fairly modular like that.
I would recommend at least trying Calibre's library management features however. First, write down all the reasons why you have to keep the books in a specific folder structure. Second, import your books into Calibre, but keep the original copies as they are. Now go through your list of reasons you need the files in your folder structure, and see if Calibre can duplicate the functionality you need. (For instance, if you find a hierarchical structure familiar and easy to work with, you can set up a custom hierarchical field in Calibre and navigate it through the Tag Browser)
If it doesn't work out, well, no harm done. Delete your Calibre library and go back to doing things the way you did before.
I say this from experience. For a year I used Calibre only for conversion and reading, because I just HAD to have my books in their own directory structure. Then I decided to try things the Calibre way just as an experiment. After giving myself a couple of weeks to adjust, I never looked back.
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