I think we need to know more about the process you are using the CMM for.If you are establishing an X or Y datum you would use the probe on the sides of the workpiece and if you were probing the surface to establish a cutting strategy for a similar radius ball end mill,you would be using the centre of the spherical radius to establish a toolpath.For inspecting a 3D surface I would expect a parameter in the CMM software to enter a tip radius/diameter from which surface offset could be established for comparison with the surface CAD file.