How I do it:
layout where you want the pins to attach to the body - I use a mechanical pencil to trace the wing attachments or simply measure out the locations
drill the holes in the body
hold or tape the wing in place
using a pencil or a drill bit from inside the body mark the pin locations on the wing
remove the wing, drill the holes and install the pins
mount the wing to the body after paint
The rear wing on this Barracuda is pin mounted using this technique.