If it's small, it's as easy as: mix, apply, dry and sand.
(for holes smaller than a finger nail)
For larger holes you will want to use a fibreglass patch over it with bondo.
But before you even do either, you must strip all paint down to bare metal, either by sanding, or using a paint stripper. Then clean the area thoroughly before applying filler (or "bondo" as we like to call it).
if you've got access to a welding machine i'd say stay away from the fibreglass . just cut pieces fo sheet metal that are the same size as the holes or smaller and tack them on, let it cool down and then body fill 'till your heart's content . if you want to do your side mouldings, do it the same way.lemme know how it goes.
urghhhhhh this really pisses me off if you havnt done it before especialythis kinda work dont try it, u should spend about 300-500 to shave off your trunk and if u F*&K up its gonne cost more because the labor and all that, if you havnt learned this from someone DoNT TRY