I square up my quilts by putting borders on. I measure through the middle of the top, then at 1/4 and 3/4 spacing across the top. I get an average of those measurements and cut my borders. Then I fold the quilt and border into quarters and pin the borders on. I ease the fabric of the top as I'm pinning. Usually the top and borders go together easily, but I have been known to resew a few of the seams right at the ends where the threads have either pulled out or to take in a couple threads. Once the top and bottom borders are on, I do the sides in the same way.
I repeat this for each border I put on.