ATI says that no prom changes are required. Not sure about paxton though. If you really want to get the most of your setup then you'll need to rework the fuel and spark tables. There is no way around it.
For example, my buddy has an ATI procharger on his l98 IROCZ. It ran ok on the stock tune. Just the addition of the s/c he went from running a 14.9 to a 13.9 (standing 1/4mi). That's not too bad at all. But with tuning he is going to run about 13.5 . The car ran "fine" but it runs way better now.