When you set them up, you can make sure you still have good throws on the surfaces. If you can't get enough throws, don't use flaperons. You will probably find that they don't help as much as you wanted.

As for ail rudder mixing, you can either use the computer for it, or do it manually. I prefer to do it manually on power and mix it on something like a glider. If you use the computer to mix, make it so you can turn the mix off with one of the switches.