you would need to know how to design circuits, pcb's for the purpose of your project, then get them printed from a manufacturer.
for example, the rapid fire for the 360 controller, at first the devs tried multiple ways using just wires, and possibly a vast array of different components. once anyone gets the result they seek, they would make a diagram and start working on getting the pcb's printed.
i believe it all essentially comes down to pcb design, knowledge of electronics, and understanding the systems architecture, which is key!
i will say, i do believe that designing a modchip, (without copying another design
) could be more tricky.