I am not sure I understand what you mean, but this is a thought: I would use a walking foot, specialy if you have batting between the layers. Pins are not enough to hold it in place. What I also do is a big X in the middle of each block before I put the strips together. That also done with a walking foot. You can do any other quilt design. I find that just a big X gets done faster and if the flannel is printed, nothing else you do will show, so an X is easier.
That being said, even with the best walking foot you will have a little shifting. How big are your squares? With large square (7 - 9 inches) even if there is a little shifting it is not noticeable at the end. You will have the seam allowance exposed and cut to fray and those ends will curl when they fray. No one will notice that they shifted. To tell you the truth, not even you. The fraying and curling will also hide if the corners don't match.
About 3 years agoI had a group of co-workers at my house, all medical technologists, none ever sewed in their life, but the lab manager's son had cancer and we wanted to make him a quick quilt to take to his bone marrow transplant. It ws amazing to see all these girls cutting (one cutting fabric, one cutting batting), sandwiching the layers, sewing the X and asembling the strips. Very few corners matched, but I kept saying that the quilt is very forgiving. At the end, while DH cooked dinner we sat around the table and clipped the edges. While we had dinner the quilt was washed and dried and by the end of the day we had the most amazing quilt for the boy, now a junior in college, doing great. As a result of this day I now have two quilting buddies. They went the next day and got their own sewing machines, joined the guild and take classes all the time. It is the greatest quilt to make.
Maria