You can attempt to get a seat in the upper deck by entering your coach preference as C1U, C2U etc - the upper deck is treated as a separate coach by the PRS with the suffix U after the coach number. The lower deck and mezzanine have the suffix L after the coach number. I have booked several times using this method and have always got a seat in the upper deck.
However, it is better to try this at a counter as you can find out (before paying for your ticket) whether you are getting a window seat in the upper deck of the coach you have requested.