Your PCB milling machine, just like any CNC machine, expect long learning curve, broken expensive bits as you're trying to learn, and make notes of combination of speed/material that will work for your specific milling job.
+1 on dedicated computer for this task. My CNC computer is still an old Win2000 with IDE drives and parallel LPT port.
But overall, I think your company is crazy wanting to go this route vs. just sending PCBs out for prototyping. Waste of money, time and manpower if all you want is a simple PCB prototype.