I also don't use a a screen protector. My 7 year old loves the drawing app so he is always scribbling away with the stylus and there are no scratches yet. I'm sure he presses a lot harder than I would ever dream of so I'd say the screen is pretty tough!
I use Calibre for almost everything, the only thing the Sony software is good for is ordering a collection so that is appears in a certain order in the reader. This is handy for my "to be read" list which is over 50 books now.
I don't have a skin for it and the only place it has been is the barn where I'm probably a bit over-protective of it