There may be another way to line up images for comparison, but this is the way I have been using. Reason: I need a number of icons based on the same starting point with the elements in the same place on the icon.
I move the image (magnified) to one of the corners of the edit pane. Then when I switch between images, they effectively overlay each other. However if I do anything to the image, Paint.Net decides that it knows a better position for the image in the pane and its really raising my temperature. Is there another way of comparing images in the way I want?