The lower half of the flange sits on top of the shingles.
Install bathroom fan roof vent.
The master bathroom and the 2nd bathroom vent through the roof and through the same opening.
The 2 pipes one a 4 master and the other a 3 2nd do not go through the ceiling but into a common box that goes through the roof.
Use an extra long 3 8 inch diameter spade bit to bore a reference hole through the ceiling and into the attic.
If you vent through a soffit where attic vents are often located the moisture will get sucked back up into the attic or roof venting.
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The 2nd bathroom vent drips on the floor and is ruining the ceiling.
From inside the attic drive a nail through the roof directly above the bathroom vent fan.
If you vent through the roof condensation will drip back into the interior.
Secure the vent flanges with roofing nails before installing the shingles.
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I recommend that my clients vent their bath fans out a gable wall if at all possible when not using an hrv or erv that is.
For optimum performance locate it between the shower and the toilet.
Slide the vent under the shingles so they cover the top half of the vent flange.
Center the nail between two rafters.
Apply a bead of asphalt roof cement on the bottom of the vent.
Draw a mark on the bathroom ceiling where you d like to install the vent fan.
Climb into the attic and clear away any insulation from around the hole.
This video is a comprehensive rundown on how to install a roof vent on a pre existing shingle roof.