Once you have the three files (The image, the 2D points and the 3D points) you can then load them into the calibration utility.
First load the image, this is strictly speacking not required but is useful as a sanity check. File->Open Image
Then load the 3D points File->Load 3D Points
Then load the 2D points File->Load 2D Points
You should now be able to check the 2D points are at the locations you expected, they will be divided into three sets because the automatic method uses three faces of a cube, but this is not really important here.
Now proceed to the calibration section
The Automatic detection method grabs an image from a Player server, so you will need to run one on the computer which has the camera attached. (player ~/PlayerConfig/1394.cfg on gin if you are at the UoA Robotics lab)
Once this is running fire up the calibration utility. Enter the server address in the lower left box and the camera index (probably 0) in the box next to it. Then click acquire, once you have a good shot of the calibration cube click acquire again and automatic processing will begin.
After its chugged away for a while the detected points will be displayed, confirm they seem correct then proceed to the next section.
If you dont get good points then use the Show stage button and stage spin box to get an idea of what went wrong.