I generally square my quilts after quilting, but this one is a little different. Actually, all they're asking you to do (as thimblebug6000 said) is get rid of the excess fabric ends that are sticking out. I'd trim it as directed in the pattern and then quilt it. I would hope that something this size would require very little squaring after it's quilted, but hopefully you could dampen it and pull it into shape if that's needed.