Indeed, I'd assume it would be a case of getting the pinouts of the pad/stick you wished to use and modifying them to the port on the back of the pad.
That's why I intend to use a 15 pin VGA cable instead of the 9 pin mentioned in the tut - that would give me enough pinouts to be able to utilize up, down, left, right, start, back, a, b, x, y, black, white, l, r.
Due to the limitations of a VGA cable (only 14 wires, no pin 9) this means that I cannot assign the rthumbdown and lthumbdown buttons without using NAND gates etc.. but hey, no biggie.