The firmware has the brightness code commented pretty well, that should be the easy part :)
For programming, you’ll probably want to solder (not needed, but more reliable than smooshing it into place) some headers to the board at the ISP pads (the 3x2 unpopulated pads on the board), so that you can easily connect a programmer to it. There’s lots of tools that will let you re-program the microcontroller (check the exact model through the labeling on top), but perhaps the easiest first step would be grabbing AVR Studio (Link is for AVR Studio 6, older versions are also available). See also the forums where there are some existing discussions about reprogramming a ClockIt :)