This photo shows significant damage to wood framing from water intrusion at a through-wall scupper. Poor or missing details—including a lack of exterior counterflashing over the scupper and poor installation of the weather-resistant barrier—allowed water to leak in from the exterior side. In addition, the scupper was initially installed with the drain-end of the tube higher than the deck. This caused water to pool in front of the scupper, and eventually that water seeped in past the poorly applied deck coating and around the scupper.
Note that the L-flashing laps over the scupper flanges and that these laps are bedded in a polyurethane caulk.
We nail-off the flange with 1 1/4-inch stainless steel ring-shank coil gun roofing nails, which provide considerably more holding power than the cheaper smooth-shank roofing nails.
Prior to applying our primer and waterproof top coating, we sand the interior of the scupper to promote adhesion of the coatings to the metal. This prevents the coating from debonding as the copper oxidizes, as it has on this scupper in photo.
Leaks at drains often occur because the original contractor had used the wrong assembly, such as a toilet closet flange ...
We replaced both of those drains with commercial deck-drain assemblies, like the ones from Thunderbird Products. Then we cut and fit metal lath around the flange without allowing the two metals to touch.