I know exactly what you mean. I've done this before, it wasn't really hard, but I've tried to type the directions up 3 times and it is REALLY hard to explain!
Basically, I pieced the window parts, basted them together to make a grid/lattice and laid them it the uncut fabric and made a mark where the raw edges of the windows touched the focus fabric. Then I removed the windows and measured 1/2 from the original marking. This second measurement would have been covered by the window fabric (make sense?) This is where you would cut.
The half inch allows for the seam allowance. Seems like you would only need to add a 1/4 inch, but that's not the case.
Try this with some scrap fabric first.