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There is no 'should' here. Do what makes sense to you.
People use calibre for one or both of two reasons: to convert books, and to manage their library. If you use it only for the first, then put the converted books in a place that makes sense to you. If you use it for the second, then let calibre manage all the books, included the ones purchased from Amazon.
It seems to me that managing some of my books with application A and some others with application B (e.g., kindle-for-pc and calibre) is a recipe for confusion. That may be because I find myself easily confused. Perhaps it makes perfect sense to you.
Keeping the amazon books in the kindle-for-pc folder (or wherever you downloaded them to) after adding them to calibre is a personal decision. I wouldn't, but that is irrelevant. Again, do what makes sense given your usage patterns.
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