I disagree with Bob that the emblems should always go back on. It's a decision that should be made by the designer and the owner of the vehicle. We leave the emblems off more often than not. Typically, they get in the way of the wrap layout. If there are holes, we deal with them on a case by case basis a few different ways. It depends on what will look the best and last the longest.
Sometimes we cut small circles of magnetic material, place it over the holes and wrap right over it. Other times we use plastic hole plugs. They are available in black or white and in a variety of sizes at your local hardware store. They work great and in most cases, don't interfere with the design.