I download books from Amazon to my Kindle in the usual way (ie Wi-Fi or 3G).
Amazon books always end up in the Kindle Documents folder all together. Connect Kindle to PC (that has Calibre on it) - Upload the books from the Kindle by going to the Kindles Document folder.
When downloading books from Calibre to Kindle they will be filed under documents under the Authors name (not all thrown together like the Amazon download).
mitch13
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