When you run the transmitter wizard, it tells you to wiggle this stick, or toggle that switch. When you do these things, it watches to see which channel moves, and assigns the detected channel to the wiggled function. This means that you can plug the channels in, in any order and it will figure it out.
Another thing I would like to mention is that there there is Arming set up in Configuration -> Input -> Arming Settings. You must select a way to arm it there. You must arm it or the motors will not spin.