Place the person layer on top of the layer with the bullet holes.
If you don't have the person on a separate layer from the background, you have some work to do, probably rotoscoping.
See this page for an overview of compositing:
Start here to learn After Effects: http://adobe.ly/bjBT3P .
I was thinking I was going to have to shoot a scene with green screen so I could make the character background seperate. Thanks for the input. Do you have any good tutorials on rotoscoping you know off hand?
If you haven't already shot the footage, you should definitely shoot the actor against a green screen. Rotoscoping is for when you haven't done that.
See the link that I gave for a good place to start for information about compositing techniques, including keying footage shot with a green screen.
It's all layers. It's the same thing as cutting things up with scissors and arranging them in a collage. You just need to lay a cut out of your actor over the bullet holes to hide them.
For bullet holes the masking required wouldn't be very hard to do or require time consuming roto if your camera is locked down. Just duplicate the footage layer, place some bullet holes on the top, lock the bullet holes layer, then, when the actor starts to move in front of a bullet hole create a mask that covers the bullet hole where it overlaps the actor. Make the mask big enough to cover both sides of the actor. Now move forward about 10 frames and animate the edge of the mask so that it follows the edge of the actor. Keep going until the bullet hole appears on the other side of the actor. Now move your masked footage above he bullet hole layer. If you want to use mask clean up tools then make the masked footage layer a track matte. If there's a lot of motion blur just feather the edge of the mask. If you have a bunch of bullet holes that are animated and you want to use the track matte then select them all and pre-compose, then apply the track matte to the pre-comp.
With a locked down camera and a quick movement by the actor, this should only take you a few minutes. It will be much easier than trying to shoot greenscreen and pull a key, and match lighting, and clean edges. Greenscreen only really helps save time when you're replacing everything behind an actor. A few bullet holes wouldn't be worth it.
If there's camera movement then the technique is exactly the same except that you'll need to track the camera movement and apply that to the bullet holes so they don't float on the wall.
One more hint. You should judge the effectiveness of your shot watching playback in real time instead of stepping through the shot a frame at a time. The motion of your actor and a little feathering will hide a bunch of roto errors that will stand out if you carefully look at a frame at a time. Keep it simple.
Thank you both very much for your input, it has been very helpful and was exactly the answers I was looking for.