1000x1000 waste board help

im trying to put a waste board 3/4 mdf on top of the actual waste board i tried using this project for holes to line up
http://easel.inventables.com/projects/e3AhAU3oZ7Sw9ml_XVc9Ug

but it seems that its off all of the holes dont line up correctly

does anyone have a better project or the spacing of the holes thankyou

thank you

make sure your X & Y axis are calibrated too.

thank you i just did a check did a 1 inch by 1 inch square at the 2 inch by 2 inch mark came out great