Hockeynut--It's my understanding that Calibre won't be able to transfer anything you bought from the Sony store. (I've never tried it, so I'm not 100% sure about this.)
But, I use both Calibre and the Sony Software to transfer books to my 505. So you would be able to only use the Sony Software to transfer the books you've purchased from Sony Connect and Calibre for everything else.
dordale