Keith,
I'm not familiar with the steps involved on an International Metrology Systems (IMS) or their Virtual-DMIS product. However, it would appear to me that once you have aligned the part to A B & C you should be able to report the holes location. As far as the bonus calculation applied, that is simply the amount in size the hole has grown from the minimum allowable hole size. If your diameter is 12.0mm plus/minus 0.5mm and it checks 12.3mm then your bonus is 0.8mm. (12.3 - 11.5 = 0.8)
Regards,
Geoff
Sr. CMM Programmer
Lapeer Metal Stamping
LMS Metrology Lab
Lapeer, MI