Funny you should ask that today... I have never before squared anything up on the wrong side. Like Roben said, I want to see the seams and there is one, or more, reference points in the block that I always want at the same measurement so they are all the same.
But, last night squaring up a bunch of HSTs that had either the same fabric on each side or two dark fabrics it was difficult to tell exactly where the seam was so, I turned them over and I am lining up the 45 degree angle on the thread line.