I have looked at PCDREH website and as far as I can see the connection to your computer is a SERIAL connection using rs232/USB.
Mach 3 uses the 25 pin PARALLEL port (the printer port) which has seperate outputs (12 in all) and inputs (5 in all). Signals to drive your stepper motor cards generally go out in pairs (one step pin and one direction pin) for each axis. Therefore the x axis would use pins 2 & 3, y axis pins 4 & 5, z axis pins 6 & 7. There are then spare pins to drive your spindle controller, your coolant, and the input pins carry signals from your spindle encoder, and your limit switches.
The system uses the parallel port because of the speed, and closer control on the relative movement of the axis.
Your really need to download the tutorials on connections to the computer, which will explain it all.