Shingle your roof up to two rows shy of the soil stack. The flashing end of the soil stack must attach to the sheathing of your roof.
Clean the area around the soil stack with a broom. Remove all traces of debris and dirt to allow the flashing to rest firmly on the roof.
Slide the roof jack over the soil stack. Nail the flat flashing at the bottom of the roof jack to the roof sheathing with roofing nails and a hammer. Apply roofing tar over the nail heads with a putty knife. Spread roofing tar over the circumference of the flashing with the putty knife, spreading the tar an inch on each side of the seam.
Continue laying the shingles on your roof. When you get to the soil stack and roof jack, cut the shingles to fit around the pipe. Once the shingles are installed around the soil stack roof jack, spread roofing tar at the seam between the roof jack covering the soil pipe and the shingles.