Bend the new sliding door's flange, running around the door's perimeter, out. Place a tube of sealant into a caulking gun. Cut the sealant's tip off with a utility knife.
Spread two beads of sealant around the rough opening. Spread the first bead approximately 3/4 inch in from the opening's exterior edge. Run the second bead about 2 1/2 inches in from the first bead of sealant. Place a third bead of sealant around the back of the new sliding door's flange.
Lift the sliding door into the opening and center it. Position the door's bottom corners first then push the door up and adjust the top corners. Hammer a 2-inch galvanized roofing nail through the top flange, near the center, to help hold the door in place.
Place a level on both sides of the sliding door to check that the door is plumb in the opening. Finish hammering 2-inch roofing nails through the door's flange, placing one nail in every pre-drilled nail hole in the flange.
Run a strip of flashing tape over the side flanges. Extend the tape two inches above the flanges' top ends and two inches below the flanges' bottom ends. Run a strip of flashing tape across the top flange. Extend the tape one inch past the strips of side flashing tape. Push all the tape strips securely in place.
Install the interior and exterior molding around the new sliding door. If the old molding is being reused, simply nail it back in place with finishing nails. If new molding is being used, measure the length and width of the door opening. Cut the new molding to these measurements, mitering the ends to 45-degree angles with a miter saw.