By using the macro's in the instruction manual. Follow the flow chart in the manual as it can take a few tries to get it calibrated.
Calibrate X/Y/Z macro to be the same distance as each other by adjusting the end-stop screws. Then adjust the horizontal radius until the outside X/Y/Z macro's are the same distance off the bed as the center macro. Keep in mind that the center of the bed will "not" change when you modify the horizontal radius. Only the outside locations will change. This corrects any concave or convex motion of your effector.
Once the center & X/Y/Z are the exact same distance off the bed, use the menu on the LCD to set the Z-Height. Make sure you select "home" first.
Also, check out this page as RollieRowland has made huge progress into automated leveling/calibration of the Rostock v2.
http://forum.seemecnc.com/viewtopic.php?f=36&t=8698