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With regard to calibre and where it keeps its internal database, please see the description in the post linked in my .sig. The short version is that calibre is a book manager, not a file manager, so one shouldn't mess with its internal file folders. If you need access to the files directly, either use your originals (which are still exactly where you left them), export them individually or en masse from calibre, or use calibre's right-click function to go to that file. Pretend that its ebooks are actually stored inside a database (they used to be, in fact, but there were other issues). The fact that it's possible to get to calibre's files makes people think it's some kind of file manager ... but it isn't, and was never intended to be, and won't become one, any more than Windows Explorer will become a block/sector editor. That's just not what it's for.
As for how files are set up on your device, calibre's output is infinitely flexible, or close to it. You can have it transfer files to your device in just about any way, to any structure, you want them to have. If the particular style you need isn't the default for your particular device, the folks over in the calibre forum will be more than happy to show you how to set it up to do what you need.
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