I think you should set up your transmitter the way you want it. It is not hard to do. Carrell pointed you in the right direction to everything you need to do the switch over.
Having said that you may actually have an advantage being left handed and using the "normal" setup. If you use your dominat hand and learn to fly with the rudder you really will be miles ahead of someone like myself. Once my instructor got me to the point of being able to fly the circular pattern I learned to fly mostly on my own and it was of course easier to use my dominant right hand. As a result my ability to use the rudder is marginal at best. I have been making a real effort to back up and learn to use the rudder but I have all the bad habits you get from learning to fly using the ailerons. On landing approach good rudder control is very much an advantage.