Decipher Serial Port communication log of microcontroller
The simplest way to do it would be to get a blank Atmega16 and an ISP cable.  

Burn the Arduino bootloader to the new Atmega16 (instructions at various places on the internet.)

Pop the Atmega16 out of the Qu-Bot and plug in your new one.  Experiment to your heart's content.

This keeps the original Atmega available for comparison if you need it.  Besides, it may no be possible to overwrite the bootloader on the existing chip.