First, start with the larger uncut square. Draw a diagonal line on the small square from corner to corner Place the small square on the large one, but don't sew on the line, sew right next to it, like a few threads away towards the corner. fold the small square over to check. if it looks ok, cut the 3back layers. if it's just a tiny bit smaller than it should be, cut the 2 middle layers out and leave the large fabric square. The slightly smaller triangle will be caught between this fabric and the adjoining block. if it's really too small, take the seam out and make your next seam even farther away than the first one.
Another technique is mark the appropriate diagonal on the larger square, and cut the smaller square oversized. sew the seam, press, square the block up , then cut the excess layers.