Good ideas here, but I'm with Marianne, it's likely that some of the grains were off when you cut them and needed to be prewashed, stretched diagonally to straighten, starched and ironed into submission, then use a walking foot if needed to keep them from getting stretched. After that, block it square before sandwiching and maybe use a little more quilting than you normally would. If the back is nice and square, and you sandwich it well, it will probably maintain squareness with quilting and blocking. Good luck there.