http://www.youtube.com/watch?v=OQq-5p8RCS8
Here is one video that demonstrates it. If it isn't clear after this one, Google "how to square up half square triangles" and it looks like there are more videos explaining it. I didn't watch the other ones. You have to use a diagonal line on the ruler lined up with the diagonal seam of the half-square triangle. If you don't have a ruler that is exactly the size of the finished HST then you will have to cut a little off of two edges then adjust the ruler to cut the rest off of the other two edges. There is a ruler that is called Precision Trimmer, that is for squaring-up and most LQS's have them.
I'm sure there is someone on the board who can explain it much better than I can and hopefully they will read this post.