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My personal opinion, Ashjuk, is that you're worried about the "backend" (like I was). I say, forget it. Who cares if it stores six bunnies, eight tulips and fourteen one pixel dot image for each book or not (it doesn't)? I don't even care how the directories work now (I used to...so much).
What matters to me is that I can whack all my ebooks somewhere and easily and quickly find them via one interface. I can search by title or author or even tags. Some people do even groovier stuff (but I've embraced my inner luddite). I can easily get them onto my gozza of choice to read them. They're in one place that can easily be backed up.
Years ago (before they were even called ebooks), I had bazillions of text files scattered all over my hard drive in what I called as my "system". That got old really quickly. After my initial brain explosion with the stuff behind the Calibre curtain, I have settled down to just letting the system (Calibre) do the heavy lifting.
My Calibre tells me I have 3969 books in my library. That's now all I want to know. I can live with that.
I don't mean to be rude or be a smarty.
How about this: what is it that you want to do but can't with Calibre? Forget the files and how it works. What is it that you're trying to achieve? I'll bet someone here (not me, obviously...because luddite) will know how to do it.
Oh, dear. I've turned into one of those rabid software evangelists. Woe.
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