Squaring up should actually take place when you cut off the extra backing and batting. What I do is use 2 straight rulers and a 45-degree triangle ruler (a T-square works great for this if you have one!) to make sure I have a perfect 45-degree corner; then I mark the corner. I do this on all 4 corners, then connect the lines in-between. I stand back and look to make sure nothing looks wonky before I cut. If I'm not sure, I re-measure and remark as necessary until I am satisfied.
Actually, after I have the square marked, I do not cut the quilt yet. I first attach the binding, using my cutting line to match up the cut edges of the binding. Only after that do I cut the quilt (making absolutely sure that the binding is out of the way of my rotary cutter!).
You can do something similar at this point, but you now have much less room for error.
I will be interested to hear how others square up a quilt in case someone has a better method than mine.