The best way is probably to download them directly from your kindle if they are amazon bought books. Like ATDrake said, if the books are DRMed, you wont be able to transfer amazon bought books over to the kindle by dragging and dropping them. The Kindle for PC has no direct association to your kindle, its just for reading books you bought from the kindle store on your pc.
If they are not DRMed books, you can just drag and drop them into your kindle folder or use calibre (a truly wonderful creation!)
Cheers!
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