What version of xCalibrate are you using? You mention the GUI, which was deprecated beginning in 2009.1 release. If you have the GUI, there should also be a manual, "xCalibrate Interactive User's Manual" (or xcalibrat_user.pdf) with instructions. The name of the section in later manuals is "Running Calibration Automatically", in the chapter "Running Calibration". It may be called something different in earlier versions; I checked 2008.4.
I can try to help a bit more if the instructions aren't working, but I don't believe the GUI is officially supported any longer.