Hi Tom,
From my opinion and from what i've seen you should definatelly install the scoops before the painting,finalize and find the desirable spot for you,cut it in the right position and have all the benefits gives you an unpaint car.
A friend of mine have made a similar installation as yours(suby engine + side scoops) and he paint them in the same color with the car, which is totally beautifull.
Check more here
www.bugaru.gr .
Friendly,
Jim