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You'll get answers regarding the import, etc., from gurus much gooier than I, but there's a bit of it I can address. Namely, the questions about the calibre library and folder structure.
You shouldn't be worrying about how calibre organizes its files. As it is usually put, treat the calibre library folder structure as a black box. Don't even peek in there. Once you're using calibre, you shouldn't have to even think about those folders existing. Just interact with them through calibre itself. Like most people, I was accustomed to using my filesystem for metadata before I started using calibre; it quickly became obvious that using calibre (and real metadata) was so much easier and more efficient that I would never want to go back to the old way.
The tag system alone can beat any folder-based model all hollow. Let's say, for example, that you have a book of short stories by a favorite author, and they are a mix of genres: some fantasy, some science fiction, even a couple of mainstream mystery stories. If you were using the filesystem for metadata, how would that be categorized? Fantasy? SF? Mystery? With calibre, you just tag it as all three, and it'll show up in each category.
Or how about a book by two or more authors? In your system, which folder does that go in? With calibre, you don't care, because you just do an author search for whichever author you want and all of his books show up, even the ones where some other author's name was first on the cover.
You want to give a friend something ... say, all the fantasies from the Baen Free Library. So you select the tags you've set up for "fantasy" and "BFL" and export the books to wherever you want them. Bingo! Ready to go! No need to rummage through your folders trying to find the right books, or remember if this particular Mercedes Lackey book is redistributable or not; it's all in your tags.
With regard to the waste of space from duplicating files (if you don't delete the originals), I have somewhere around 2200 ebooks at the moment, of assorted sizes. They take up about 1GB. So your 8000 files can be expected to fit reasonably well into 4GB of space. When you figure that a 2TB internal hard drive currently sells for $130 (and with free shipping) on buy.com, we're talking around 50 cents worth of storage space. Or you could go the luxury route and spend eight bucks on a flash drive.
I'd guess that you, like me, remember the days of the cake-box RMO5 disc packs with their then-unimaginable 300MB capacity. A few GB here or there doesn't matter much anymore.
Calibre is an amazing tool if you use it as it was intended and work with it, not against it. It's a way to manage your books, not your files. Just keep that distinction in mind and calibre will be your devoted ebook slave.
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