I have done it both ways, including the ailerons and excluding them and ended up with flyable models every time. I will sujest you exclude them for your first ballance point attempt as it will give you a more forward C/G. If you have oversized ailerons your C/G could be moved dangerously far back. Small 1 inch strip ailerons (common on trainers) would have little effect (.25 inch).

Check this out. I've used this too.

http://www.geistware.com/rcmodeling/cg_calc.htm#cg