If you were just beginning the project, and were only considering using the Arduino to control the motors, it might have been simpler to use a motor controller with a USB input, so you could control it directly from the PC, such as Pololu Simple Motor Controllers.
However, since you have the Arduinos, it is more a matter of how to use them. In general, you write a small program on your PC, that opens up COM4, and reads from standard input and writes to COM4. For example, I believe PuTTY under Windows can do this: http://www.ehow.com/how_8733462_use-putty-serial-connection.html.