I took a quick look at the pattern and I have a couple of thoughts. It looks like to me that the square-in-a-square should be 4 1/2" unfinished. Use any technique you prefer to make the units and the flying geese units (2 FG sewn together) should be 4 1/2" unfinished too. So each FG unit would be 2 1/2" x 4 1/2" unfinished. Use your Accuquilt to cut those individual pieces.
Here's a chart & guide for SIQS units:
http://quiltville.com/sqinsqtutorial.shtml
Hope it helps!