Calibre is great for transferring files to your Kindle. That's what I use as well. Only reason I can think of that you wouldn't want to do this is if you use multiple Kindle devices--you won't be able to sync your position on books side-loaded through Calibre. (Someone please correct me if I'm wrong. I'd love to know if there is actually a way to sync content that's been side-loaded to Kindles through Calibre.)
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