You can put them on top of the wrap. In my case, the person that did my xpel later put the stickers on some extra xpel trimmed to the exact size, and then put that on top of the xpel already on the car. May sound silly, but made it easier to adjust to get it just right when applying, and he said it'd be easier to remove without damaging the xpel underneath, should the need ever arise. You can't tell it's on a double layer.
jsm - it really is only an issue if you have the rear bumper applied with paint protection film (aka clear bra). If you do, then applying the stickers on there is no problem, but do keep in mind that if the film is ever damaged and needs removal, you will need to reorder new stickers as they will come off with the film.