First of all, the CAM program is what takes your CAD drawing and applies machining strategies and toolpaths to it to produce a G-code program - it does not send any signals to the drives (at least not in this context). That's the job of the CNC-control program which is what EMC2 and Mach3 is - for example.
All you really tell the CNC-control program is how many steps it needs to send out to produce one unit (be it an inch, mm, foot, um, degree or whatever) of motion. It is the drive entirely that handles the microstepping of the motor. If you have 1000step/unit with a full step drive you have 2000steps/unit with a halfstep drive and 10000steps/unit with a 10uStep drive and so on.
Microstepping is achieved by varying the relationship between the current thru the windings in a SIN/COS manner. There are plenty of application notes etc on how this is done, take a look at the Alegro site for example. They don't show you how to do it with a PIC but they show you the theory.