AFAIK there is no magic way to do it. It's an iterative process.
1) Print your calibration object
2) observe which axis (or axes) is (are) off
3) adjust the machine
4) repeat
You need to make sure that the print head is the same distance away from the bed both on the left and right and in the front and back, but you also need to make sure that the Z rods are perpendicular to the print bed