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Calibre can be intimidating at first. However, there is a separate forum where people can answer your questions. It has loads of features, but you don't really have to use most of them if you don't want to. There is a 10 minute video tutorial on their website that provides some basic info.
The best way to back-up the reader may be for you to use ADE to manage your books. Then drag and drop the EPUB/PDF files from the Digital Editions folder to the Books folder on your Sony through Windows Explorer. It doesn't help with the notes though. It was easy to back-up notes with the earlier models, but the T1 firmware is organized different so no one has posted a method yet that circumvents the Sony software.
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