The first thing you will want is to insure concentricity of the probe tip to the spindle. There is a proceedure spelled out but I just prefer to touch a small .0001" indicator to the the side of the probe tip and spin the probe by hand with the wire disconnected. I then adjust the set screws accordingly.

Since I reference all my tool lengths to the probe I put the probe in my tool height gauge (while electrically connected to the machine) and compress the tip vertically till the light comes on and then enter this value into tool 99 for the probe.