They aren't talking about programming the Arduino, but instead having the Arduino provide a simple text interface on the serial port. You would read input, have a real simple syntax to read or set values that are stored in EEPROM. Then you can provide a simple GUI interface that would talk to the device as a terminal. While you are debugging it, you would just use the serial monitor.
I gotcha. That sounds interesting. I use the serial monitor quite a bit when debugging but I'd never thought about having the user interact with the USB interface. Humm are their some examples on the net somewhere? Give me some ideas on how to get started with something like that. It seems like that would be a nice way of getting custom values input for complete flexibility.