How do I fit window inserts if my windows aren’t square?

If the windows aren’t square then you may be better off going with one of the windows made from plastic sheet rather than the Innerglass one which is made from glass. The InDow one comes with a measuring kit that explicitly accounts for non squareness by measuring the diagonals as well as the horizontal and vertical parts. The frame of the Window Inserts one is so flexible (flimsy you might say) that it would probably accommodate any deviation from straight up to at least an inch, even without explicitly accounting for it.