One thing: never run the Sony Library software and calibre at the same time. They get into brawls over whose turn it is to write to the device database, and the results get ugly. Make sure you have Sony's software set to not auto-start when you plug in your 600 (I understand there's an option for it now; I had to disable the old version with msconfig).
Calibre can move DRM-restricted (that's the accurate term, by the way, not "protected") around, so it can manage them along with your DRM-free books, load them on your 600, etc., but it can't convert them or view them. This is why friends don't let friends buy DRM-locked ebooks.
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