Get the Latest Firmware from Here
Unzip all the files into a folder.
Plug your programmer into the board using the 6 pin connector:
Click for Picture
In the folder are two .bat files. Depending on the programmer you have, you can either run them or look at the contents for the command line needed. The pololu programmer assumes the USB is actually a COM port but the USBasp programmer has a USB only protocol. Avrdude is the program that does the actual programming operation. It will accept parameters for both types of programmers. However you will need to know the COM port if you are using the Pololu (or similar) units. You can find that out with the device manager in windows. If it is different than what is in the prog.bat file you will either have to enter the command line yourself or modify the prog.bat file.
Mac users, a similar procedure is required, go to this link for more information on setting up a programmer on your machine:Pololu Mac AVR programming