This is a pretty detailed how-to make HST's. I think you should read it first to get an idea of the most common method. The beauty of this method is NOT having to deal with any actual triangles and bias edges.
http://quilting.about.com/od/quickpi...squaretria.htm
Generally the math used is to add 7/8" to the finished size.
So if you wanted 2" HST finished, you add 1/2" for the seam allowance, and then 3/8" for the angle.
I prefer to cut the squares adding an inch or more to the finished size. So let's say 3 - 3.25" squares. Then make the HST and trim them down to the actual size. I find it makes a more accurate block, without having to bother with a 7/8" measurement. Also, if you make a slight error in the cutting, the square still wouldn't be the right size.
Others may have different opinions.