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I must echo Chris's views strongly:- wing veins are useful but you waste your time using them unless you use other characters as well.
Even within a species there can be considerable variation
Even within an individual there is often variation:- the two wings being different:- this is a consequence of the fluctuating assymmetry that can be important in how flies evolve.
Re use of photoshop:- I have played with image computational approaches to quantifying morphometric characters. :- creating layers will not help you unless each image is exactly in the same plane, even using Montage , FDR and other image tools there are image registration issues which are only fixed by applying algorhythmic fakery.
Its fun playing with these things but don't take them too seriousely. I recently used an FDR approach to merge wings from a group of empidid species and so come up with a 'ground plan' for the group. The results were visually interesting but scientifically irrelevant!

In summar, use a key and forget about the computer

cheers
Adrian