The trick here is to cut the size of the square or rectangle to a certain dimension so that the scallops will come out even.
Here is the best tutorial I have seen on this so far.
Also, I find it best even when cutting just one side, to make a mark on your cardstock at the halfway point on the side you want to cut, insert the paper and turn the punch upside down and line up the punch on that center mark, then punch. Now you can turn the punch over and contine down each side as you usually would. This way, you come out even on both ends.