Don't have any suggestions for you on the layout but I'm also using Joan's cathedral windows pattern too. I can say one thing, sew the flaps before you connect the blocks. I put the blocks into rows thinking I could go back and stitch down the flaps then and its a pain to do and I have 5 rows of 9 blocks plus once I start connecting the rows I'll have another row of flaps to stitch down. Not fun is all I can say.
Good luck on your venture.