Okay, I'm not very good at this so if this is a stupid idea, you can just disregard it. Why not just make the piece in between the two small squares a bit wider so that the small squares are even with the edges of the rectangles? It seems like it would be a lot easier to piece if the two small squares lined up on the outside the edges of the rectangles.
Anyway, that's what I would do but I've been known to do things in a rather, um, unconventional manner before . . .