Derek,
First of all, the only stupid question is the one that doesn't get asked. What plane are you setting the ailerons for? How you align the ailerons is going to depend on the type of wing you have. I'm going to take a stab at this and assume (you know what they say about that!! ) that it's a trainer with at flat bottom wing. If this is correct you will align the ailerons so that they are level with bottom of the wing. If you have a different type of wing let me know. Take a look at the attached pictures. These are from a Sig LT-40 that I'm building right now. I have a build thread going on it if you are interested, you can find it at [link=http://www.rcuniverse.com/forum/m_3439708/tm.htm]Pay It Forward built. Sig LT-40[/link] . You can see in the pictures how you can use 2 pieces of wood and a couple of clamps to align your ailerons with the bottom of the wing.

Is this an ARF or a kit? If it's a kit the cross section of the wing drawing should show you how to align the ailerons.

Hope this helps

Ken