Has anyone had issues with the remote buttons not runing the motor in witch it has been labled?
Care to post your code? Probably a problem there in syntax or logic.
Edit: I think I misunderstood. This is pre-fab code from Vex? I think the best and easiest solution is to figure out where the motors should be to run what you want, and leave them there. Maybe write it down somewhere.
Easiest / quickest way (without programming) is to do what he mentioned above - test them all, write it down, plug into ports according to what you want within those limitations.
Ideal way is to write a code (or start by using a sample code), decide what you want ports to be, and put them into the program and the robot as you prefer.