I have both Calibre and SONY's software installed. I used them alternatively - but I am careful not to plug my prs-900 via USB when Calibre is open - it likes to upload files and to mess with my organization of files. Basically, I use Calibre to download magazines and newspapers from websites as e-pubs (nice to have the Economist on my prs).
I think using both software to upload files is a bit tricky, so I upload everything via SONY's interface. I would rather do everything via Calibre - but I have not yet found a way to view my pdf annotations in Calibre, which is important to me. And using them alternatively to upload files... maybe I just didn't figure it out... but it seems to mess things up.
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