No, Amazon does not back up books from other vendors.
Start by turning on your wireless so that Amazon can copy your notes and clippings for your Kindle books. Then copy your entire Documents folder from your Kindle to your computer. You can then delete any books you bought from Amazon (for me, those are all .azw and .tpz) and their associated .mbp files, but keep any samples (you can tell which are samples by sorting by file size). Samples aren't backed up at Amazon and they have no DRM. Amazon books do have DRM, and you'll need to re-download new versions for your K3, so you can delete those. Your notes and clippings on Amazon books are saved at Amazon; notes and clippings on non-Amazon books live in the .mpb files, so be sure to save those.
When you get your K3, copy your Documents folder back over, and use the Archive to download any books you want back on your Kindle right away. You can also copy your Collections, and any Amazon books on the device will go into their Collections, but you will probably need to re-do Collections on non-Amazon books.
That should cover most of it, I think!
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