Weezel (sorry but somehow that has a nice ring to it when i type),

Go to DirecTv's website and there is info on how to do this. In short, you can associate each box to a different IR code so each one responds to a different remote. But in order to be of further assistance and not flame you by saying "hire a pro" we would need the whole thing spelled out--box model numbers and how you are using these boxes.