dbareis,
Calibre's source code requires: those files, in that location, specifically structured
and named "as is".
The absolute only way you're going to successfully change the structure is to learn Python programming, fork calibre (and any extensions you might want to use), and produce a custom build of the program. But I would not expect too much assistance in any resulting difficulties.
BTW, I should mention that probably half of the new users in these forums go through a "change the file structure" phase. No one has succeeded yet. Because, other than mucking about in the files, there is no reason to have your preferred structure within calibre's library. You might want to see a specific structure when you
export them. Or, when
displaying them. But the actual file structure, name and location as used by the database? Nope.
Remember, calibre's library is meant to be a back-up that you don't directly touch. It is not meant to be your one and only copy of these ebook files.
Please take a look at the
FAQ, particularly questions 2-4.