Well, in both cases you want to keep the PWM wires / traces away from the other wires / traces. In a fancy multi-layer PCB you would put those signals on a separate plane and put a ground or DC power plane on each side. In the proto case just use wires that are long enough to keep them away from everything else. When you do a PCB you could try to put the PWM traces on the back side of the board and keep most of the rest on the top side of the board (or the other way around).
Good luck. Sounds like a fun project.