If you've never done bodywork and/or don't want to do it yourself, just have the guy fill the holes in.
However, I would recommend doing it yourself. It's not difficult, and it's neat to be able to say you did it yourself. Here's how I did it:
First, I sanded the sections of the decklid where the holes are with an 80 grit paper. Then, I filled the decklid holes in with some bondo short-strand fiberglass filler, wait for it to cure, and sanded it smooth with the 80 grit. Make sure to check for air pockets at this stage. The fiberglass filler is relatively porous and rough, so you will need to use some glazing and spot putty on the area to make for a good, even surface for primer to adhere to. Sand the glazing putty to whatever the primer recommends (probably 180 grit), then apply several thin coats of a high-build primer. This will insure a smooth, even surface upon which the paint can be applied. The primer should be wet-sanded with a GOOD sanding block, slowly working up to 1000 grit or more. Make sure to feather the edges of the painted and primered sections so that they are the same relative height; otherwise, you will be able to see where the holes used to be even after paint.