I am working on my flannel quilt (Woolies). Since it is flannel, most of the seams are pressed open as it will reduce the bulk at quilting time. Below is a picture of how I ensure the seams align. Pin diagonally from the left side of the seam to the right, then pin straight on the right side, so the fabric won’t move as you sew. Use thin quilting pins which won’t break the needle as you sew over them. Remove pins only after you have sewn the seam. It works (almost) every time! Do the same for seams that have been pressed to one side. Notice that I am using a walking foot, which doesn’t drag the flannel as I sew it.