The first thing you need to do is set the steps per unit correctly. I prefer to calculate but you can also do it from the Settings page, you will see a button just above the Reset on that page that is called Set Steps. Just click and follow its instructions. It will only be as good as you can measure but should get you close.
One thing however if your axis are moving the wrong way as per the link Brett linked you to then you should change that first, to do that just change the active state of the Dir pin in Ports and Pins, Motor Setup.
Hood