When you say they're reversed do you mean they're on the wrong side of the controller, or that they respond the opposite direction from the one you push the stick?
If it's the former then harbourside's advice is what you need to do. If it's the latter, you need to connect to the Assistant software and look on the RC tab. Next to each of the 4 main channels (A/E/T/R) there is a button that says "NORM" or "REV", try clicking that once next to the T and E channels and see if it clears up your problem.