I am in the process of installing a supervent chimney. It has a pretty standard looking flashing for the roof. The instructions say to remove the shingles first from the area under the top half of the flashing, nail the top part of the flashing down to the roof, replace the shingles to cover the top half, and let the bottom half come over the shingles. This is all very standard, and looks just like the other 3 flashings up on my roof. But my question is this - with the other flashings on my roof (from things like the furnace vent pipe) the installer/builder did NOT nail down the lower exposed half of the flashing. This is because you generally don't want to put holes in your roof unless you are covering them with shingles or you will eventually have leaks. But the directions from supervent tell me I am supposed to nail down the flashing ALL the way around including the lower exposed half. It says to use neoprene washers or silicon sealant on the nails. I don't want to deviate from the manufacturers instructions, but I was just wondering what other people have done and if you did put fully exposed nails though your roof did you have any problems with leaks? They also don't say what type of nail to use and I'm wondering if the galvanized roofing nails that I have been using are too short to go though two layers of shingles, the flashing, and into the roofing material. I guess not nailing it down fully could cause the chimney to have some play which would not be good, and it could also give enough room for bees to fly into the catheral box below the flashing and build a nest in there, which I suppose could potentially catch fire?