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I use both. Well I use Sony software for the firmware updates. I use Calibre for organization of stuff. To convert some things from one book format to another. I fix the names of the files. Yes, you can upload files to your reader via Calibre. I seldom use the Sony software much. The older version of their software was much better, the new one is very pretty and if you have lots of books on different machines, the sync feature can really screw up your reader. (So don't let it sync unless you want it to).
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