you paint the POR-15 over the rust... if you want to fill the pits, follow the directions on the POR-15 can concerning topcoating and body fillers.
I just hit the frame with my wire wheel / wire brush after cleaning it with oven cleaner to get rid of the grease and oils. I'm not even going to bother with the rust pits, since you cant see them when the cab, bed and fenders are on the truck.
