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I like to use Calibre because it is a catalog for all my books and personal docs (mostly knitting patterns) regardless of where they have been purchased. I also love the ability to edit metadata and customize my catalog. A feature I'm just now exploring is the recipes Calibre has built in to bring additional web content to my eReader. My Kindle software is okay for what it is, but it doesn't do as much as Calibre.
For simplicity, without all the extras, the eReader software for your device works just fine too. It really is a matter of preference.
I don't know of any instance (though I am no expert) of Calibre messing up an eReader.
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