What you seem to be saying is that you are having Mach 3 running a mill on port 1. What you want to do is run another set of kit on port 2, using a different GCode program.
I do not see how you can run multiple versions of mach 3 simultaneously on the same machine.
Mach 3 uses a great deal of the computers processing to generate the various pulses, in strcit time, required for moving the steppers/servos.
What exactly are you asking.