Calibre keeps its own archive of your books. So you download a book to wherever, then import it into calibre, whereupon it goes into calibre's black box, and you deal with it through the calibre GUI, including loading it on your PRS.
I'm actually not sure how it works with DRM-restricted books, because I don't buy them as a matter of principle.
Nearly all of my books come from free archives such as Project Gutenberg, but when I buy them, I go to Baen, BookView Cafe, etc., where I can buy good DRM-free books.
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