There are many ways to do this, here is how I would do it.
Once the opening is cut to size I would place the hood in position. Mark and drill holes equally spaced all around it for pop rivets through the scoop and steel hood. Rough up both mating surfaces with 40 grit sandpaper. Get some Evercoat Vette panel adhesive and spread it on the hood and scoop where they meet. Place the scoop on the hood and pop rivet it down. You will have to work fast as the Vette panel adhesive kicks pretty quickly. Test it before so you can get an idea of how fast it is. You can slow it a bit by cutting back on the activator. Once the scoop and hood bond has cured sand the excess Vette panel adhesive away. I would not use Bondo to fill in the areas, I would use fiberglass mat and cloth. Use Bondo like materials only to fill in low spots after the majority is filled with fiberglass mat and resin.
Harwood can give you some tips on what they have found works for them also.
If I remember correctly the factory glass hood scoops were placed so the mounting flange was under the hood instead of on top of it. An opening was cut so the glass scoop could be inserted up through the opening.