I've never used one to check offsets during a program, but I've used them to manually set tools.
1. Index the turret to the tool you want to set.
2. Lower the Q-setter, and the display should show the GEOM offset page with the correct tool number highlighted.
3. In HANDLE mode, move close (within .04 or so) to the contact point for Z.
4. JOG until the tool touches the contact (the machine should stop when it touches). This should store the offset in Z.
5. Jog off the contact, and repeat 1-4 for the X.
Repeat steps 1-5 for the remaining tools.
In MDI, activate the tool offset, i.e. T0101 for a tool that you can use to face the end of the part. Take a clean-up cut then ,before you move Z, set your G54 Z offset in the WORK offsets by moving the cursor to G54 typing "Z0" and press MEASUR. Your Z absolute should now read 0.
If the diamters are incorrect, you will probably want to adjust the probe parameters to correct them.