How did you install your hood scoop?

I take it your talking about installing it in a non-functional use? Regardless, if you drill holes thru painted surfaces I would be sure to apply masking tape first and drill through that (helps prevent cracking the paint around the edge of the holes you drill) also I would use paint to touch up the exposed metal, and then when installing the screws, rivets, whatever, I would put a dab of silicone on/in the hole to give it that much more protection. I am sure others who have done the same install will chime in on whether you should seal the scoop to the hood or not, but as you yourself have stated, on a non-functional scoop, if there is no place for the water to go it will just sit in there causing trouble in the future. I would even go so far to say that for a non functional scoop I would place a very small spacer in the form of a stainless steel washer (as thin as you can find, probably along the lines of a 32nd of an inch or so to actually keep the flange of the scoop from "sealing" to the hood surface, yet not enough to be noticeable. Just my opinion. Of course if your actually cutting holes to make the scoop functional, that will be a whole different gremlin altogether.