Loopback anomalies.

Regarding:

If you decide to keep the board, reprogramming the ATMEGA16U2 may bring it to life.

My primary purpose in playing with the Arduino stuff is to learn. Therefore I think I want to apply these links:
http://arduino.cc/forum/index.php/topic,96706.0.html

But I am missing some skills which I will have to pick up. For example

avrdude -c usbtiny -v -p m328p

sounds great but is it a command line or makefile or what? I am not averse to learning so a pointer to a tutorial would be helpful. As stated I am using Arduino 1.0.2 and have both a Windows and Linux (Ubuntu 12.04) systems. What needs to be installed first, and where, etc. I am still getting acquainted with the Arduino stuff.

Thanks for all comments and help.

Edit: Session ID removed from link.