In the quilting book I just bought, it says to use the side of your cutting mat without the lines and use your ruler to measure, as looking at both sets of lines can be confusing. And, use the same ruler to cut all pieces for that project.
You should also measure the lines on your ruler because the width of the increments can throw off a cut. And then, sew a 1/4" seam stitch to make sure it's all matching.