I use Calibre as well to keep track of everything. I buy ebooks from all over so I even have custom fields telling which store its from and if it was free or paid. I don't use Calibre to transfer books to my Kindle though. I use the Save To Disk feature usually save it to my dropbox.
When I want to add books to my Kindle I use the Send To Kindle program that uploads them directly to Amazon's server before that I emailed them but the new program works much better and faster.
All books added that way are add to your personal documents cloud and you can synch everything just fine.
This works for K3.3, K4 and KT.
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