Measure once, measure twice, and measure again!!!
I understand your dilemma ... depending on the width of your window frame, if you don't allow for this, you could have a very stretched out disproportionate animal!
Start with the measurements of your finished window frames and panes.
Sketch it out on paper first. Then draw it on the printed panel with chalk.
Next do your cutouts, being sure to add 1/4" all around for the seam allowance.