Calibre can handle your library. I hardly ever use the sony software.
But even without software..
Yes, you can move files directly to a Flash Memory Card, infact pluggin in the 650 and or any sony (or other brand) into the usb of your computer presents the device as a usb device. The memory card and internal memory can be written and red to and from.
Then you can manually move file in/out etc.
As for logos a nice black sticker works fine to cover that up! I read somewhere sugar water can remove most printing off of plastic! or a mr clean magic eraser.. after awhile when you are reading from the device you will not notice the buttons, and or anything but the text you are reading. :-)
Good luck
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