I have always favored putting a roof over the top of the upper story deck rather than try to cobble a way to intercept water running through a deck. It is almost impossible to construct an adequate barrier below an existing deck without dismantling it. By building a roof over the upper story, you gain shade and protection for the upper deck (even the capability for screening), and can do a screened patio below. Everything is then fairly protected from the weather, although some water will still blow in from the sides.