The teacher in my first quilting class told me to press the seams open instead of to one side. Then it's easier to line up the seams and get a pin exactly in the middle. You might want to try an even feed attachment for your machine instead of the regular presser foot, because the even feed is more likely to keep the top and the bottom lined up. Also keep in mind that, unlike math, in quilting "1/16th is good enough;" you don't need "exact."