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Installing a skylight requires setting up a safe work space up on the roof that is big enough to carry you, your tools and the skylight parts.
Use roof jacks to support a 2" x 12" board to stand on while you work on the roof. Use 16-penny nails to secure the roof jacks to the roof members. Make sure the nails are driven into the roof joists and not just through the sheathing.
Start two rows of shingles above the top holes you drilled from inside and insert a flat prybar between the shingles to break the seal. Slide the bar and remove the roofing nails that attach the shingles. Try not to cut any of the shingles. Remove entire shingles pieces, or it may look like a patching job when you re-shingle around the skylight.
Work from the top down and remove enough shingles to work around the skylight, but do not remove the last row of shingles where you drilled the bottom holes. You will be setting the flange of the skylight on top of these shingles to allow for water drainage.
Remove any roofing nails left behind from removing the shingles.
Cut the roofing paper on the roof about 6" from where you will be cutting the opening for the skylight (Image 1). Use a level and mark lines to use as a guide between the drill holes you created when cutting the ceiling in the first step of this project.
Then, use a drill with a paddle bit to enlarge the corner drill holes; this will allow you to start using the reciprocating saw to cut through the roof. To make it easier to handle, just follow the lines and cut the hole in two parts (Image 2). Trim off any jagged edges.
Cut two 2" x 10" blocks to brace in between the rafters to have something solid to nail into (Image 1). After setting the braces in position, secure them in place from the top of the sheeting using wood screws. Then, spread roofing cement on the edges of the cutout with a 4-inch knife (Image 2) to provide a seal for the skylight.
Attach 2" x 4"s to the top and to one side of the skylight opening with screws to serve as guides for setting the skylight in place. You will eventually remove these supports, hence the screws.
Carefully set the skylight over the opening letting it rest on the top brace, then slide it up to the side brace. Once it's in place, screw the flashing down with 1-1/2" galvanized screws through the pre-drilled holes.
Apply a heavy layer of roofing sealant over the flange of the skylight. Be sure to spread the roofing sealant over the area where the flange meets the roof sheathing.
Begin installing the shingles from the bottom of the roof to the top. You may need to notch the shingles at the edges of the skylight in order to make a tight fit. They need to be pressed into place so that they make good contact with the roofing cement. Work your way up one side and then on to the next; square up the shingles before you nail them into place.