You can name the pins what you want in the sketch:
byte pin0 = 2;
byte pin1 = 3;
byte pin2 = 4;
for example.
Really has nothing to do with creating the PCB tho.
Pin Mapping was more straightforward up to IDE -0023. In IDE 1.0 it got more complicated, with more files involved, and more changes needed in pins_arduino.h. I wish it was documented, as I am looking to get a couple pins added for a '2560 design I am starting to test.