So, I ordered a new decklid panel for my '03. Do I need to fill the holes left by the prongs? And should I wax the area before installation? Let me know if there's anything else I'm missing.

 

I would for sure at least clean the area up. Waxing would be up to you but it cant hurt. As for the holes, I dont know. If the panel covers them up then I would worry about it. Maybe put some plastic plugs in them just in case some water does get behind it.