Madquilter is right, when Eleanor Burns of Quilt In A Day does Stitch in the ditch, she pulls with both hands on either side of the seam an the stitch goes on the lower side, right next to the seam. that way when you let go, the fabric relaxes and the stitch doesn't show. no direct stitching over the threads in the seam at all.
if that doesn't work for you, just stitch 1/4 or 1/8 away from the seams. make it easy on yourself. quilting is supposed to be fun!