As long as you don't use a VGA splitter, but they get the signals, from different sources (USB and VGA) i THINK they will be independent. although i haven't tried it yet! (I'm also planing to use 2 LCD, and planing to do so with a VGA card with 2 outputs.. but if you make it work with USB , some Feedback would be appreciated !! )
As for the movement of windows it wont be a prob. when you have 2 different size screes, windows 8, allow you to set the EXACT position of the smaller one, around the bigger, so imo, moving wont be a prob!