Is this the 1RC body? On mine, I had the main body and the little driver painted, but I applied colored vinyl that I get at the craft store for like $10 for a tube and hand wrapped and trimmed the rest of the vinyl on the panels for a nice contrast by gliding the tip of a fresh x-acto blade along the edges of the panels after applying a piece of vinyl and squeege any air bubbles out. I like to rub the vinyl on from one side to the other and I found a card works great for applying the vinyl on the seam of the long triangular piece so you dont get air bubbles. Try not to use to much pressure that the blade ends up cutting the actual lexan panel, a fresh blade should glide pretty easily along the edge but they tend to dull quickly so I would have several on hand. I left the spoiler and window clear. I found that the panels are a lot easier to wrap versus the body because the panels are relatively flat for the most part. I wouldnt worry about the holes in the panels, but I'd be sure to press down a bit and prick it with a tack or pin so no air bubbles appear. The screws should still go through once you mount everything.
Ehh... sorry for the rambling, just wanted to share my expirence and hoping this will help, hope the car comes out great!