How do I cut out a window in the middle of plywood and make sure its square while doing it.?

use a carpenters square to draw it out, and measure your layout from corner to corner both ways diagonally(they will be equal if the corners are 90deg). for your cut, i would recomment using a circular saw and plunging it up to within 1 or 2 in of the corners and finishing out the corners with a jigsaw or sawzall or even a handsaw.