So the fresh air intake has provisions for drainage at the bottom, there should be (3) 1/2" or so holes at the bottom, plus a slightly raised area in the plastic where water can drain out. A lot of times these things fill up with leaves and such and restrict draining.
And for lack of the correct term, there is a snorkle that mounts to the inside sheet metal (3 screws, with a gasket). It gives something for the flexible boot from the heater box to attach to inside. On the outside it is tapered, more on the top/less on the bottom, to help prevent water from getting in.
Mounting - most of the holes in the plastic have metal clips that accept screws from the inside. There are just a few screws that screw into the sheet metal from the outside.
Sealing - well the factory used a product like Plumbers putty to help seal around the holes. But most of that hardens and falls off with age. Then there was a half-assed attempt to spray some form of undercoating at the factory in the area to help with sealing/rust prevention. I generally use a small amount of silicon sealer/RTV around bolt holes when I do a reassemble.