You can blend it in or sprinkle it on top before or after the bake. For my taste, pecorino romano is saltier than pram reggiano and grana padano. You can also blend in a little aged provolone or Asiago and even stronger cheeses for different flavors. If all else fails, you can always sprinkle a tiny bit of crushed sea salt on the finished pie, but it's better to go with one of the aged cheeses.
For the base mozz, you can experiment with different cheeses and combinations until you find the combo that has the flavor and melting characteristics that fit your bake.