The kit should have originally included a template that is cut from one of the crate lids. Not having this, there are several ways to align. Lay a straight edge across the top of the wing and align the ailerons and flaps to this. The alignment is not as critical as that both sides match. Another method is to raise the flaps as high as they will go (limited by the fuselage), again making sure that both sides are the same and slign the ailerons with them. Flaps and airlerons adjusted slightly high will aid cruise speed, but will also slightly raise the clean stall speed. A third method is to align the ailerons to the tips. This last method should be avoided as most tips are NOT semetrical.
Hope this helps.