I'm embarrassed to say how long it took me to learn how to drill holes that are in the right place and, if there are more than one, to line them up so the bolts/rivets, etc fit through those holes.
Here is the right way (for me) to go about it using my windshield clips as an example:
Locate the centers of the holes in the aluminum--measure, don't eyeball it. Center punch a starting place and drill a pilot hole in each place with a #30 drill. Place the aluminum clip in the desired place and hold it in position with masking tape or duct tape; using the pilot holes as a guide, drill one hole through the fiberglass. Put in a Cleco fastener to hold it tight and prevent the clip from moving out of alignment. If the clip placement looks OK, drill through the other pilot hole into the fiberglass.
You now have two #30 holes that line up perfectly but the holes need to be 5/16" for the Hylocks that I'll use. They have a very low profile head that won't disturb the airflow as much as a bolt. These are curious little gizmos-- they are intended for tightening from one side only. A nut is tightened on the threaded section while an Allen wrench is used to prevent it from turning. There is a hex socket in the end of the threaded section of the Hylock.
Use a step drill to enlarge the pilot holes to 5/16". A step drill is self- centering and creates a round hole, even in thin sheet or fiberglass. De-burr both sides of each hole and tap the Hylocks into place in the clip. I used an orbital sander to deglaze the aluminum and cleaned them with Toluene and painted then with a zinc chromate primer before installing the Hylocks. I'll probably paint them black later.
I now have two studs in the clip which line up perfectly with the holes in the fiberglass body. Yahoo!
Regards, Neil Tucson, AZ