When I make a rag quilt, I use a square of fleece or scrap of batting for the middle of the 2 flannel squares. I then sew an X through the 3 layers. Quite frequently, my flannel squares get off centered when I do that, even though I use a walking foot. I just forge ahead because the frayed edges hide most imperfections. It really doesn't matter in a baby quilt because, as my sister in law said "they're just going to poop on it".
