From your Pantostacker screen, select the Help Button.
The select Set Screen Scaling.
You will see the Get Screen Scale Factors screen.
You want to measure the outer box on the screen. The first time I did it I measured the smaller square, but you want to measure the whole field. Hold your ruler on the screen and pull the right side and bottom in or out to make that square a 3" square. Then click OK.
You screen will now show you a more accurate representation of what will be quilted.