Measure the length of the valley from its highest point to where it ends at the eaves. Cut a piece of flashing to match this length. The flashing should be at least 24 inches wide so it covers each section of roof 12 inches away from the point where they meet.
Bend the piece of flashing to create a straight crease down the middle so the flashing lies flat on the two sections of roof, covering the joint between them and extending 12 inches onto each roof. The easiest way to bend the flashing is with a large tool called a break. Many hardware and home improvement stores have these tools and will bend the flashing for you, saving you the trouble of buying, renting or transporting one.
Cover the roof completely with tar paper. Begin at the eaves and work your way up, with each row of tar paper overlapping the row below it by at least 6 inches.
Lay the metal flashing on top of the tar paper so it is firmly seated on top of the joint between the two sections of roof. Nail it to the roof with roofing nails. Only drive the nails in along the edges of the flashing that shingles will cover. Don't put any nails in the center of the flashing. Cover the head of each nail with a glob of roofing tar after you have driven it in.
Shingle each section of roof as you would a normal roof; however, trim the shingles that overlap the flashing so you leave 4 or 5 inches of the metal exposed between the central crease and the shingles on each side. Trim the shingles neatly with tin snips to leave an attractive and professional-looking roof.