Cover your roof substrate with a moisture barrier of tar paper or other material, according to the roofing manufacturer's recommendations.
Set the first piece of valley trim into place at the very bottom of the juncture between the two surfaces of the roof. The edge of the trim should overlap the eave by 1 inch. Secure the trim in place with a pancake screw on both edges every 2 feet along its length.
Place the next piece of trim just above the first one, overlapping it by 4 inches. Fasten it in place the same as the first and continue, one piece of valley trim at a time, until you reach the top.
Place an expanding closure strip along both sides of the line of valley trim, approximately 1 inch in from the edge. Install the flat roofing panels on either side of the valley, positioning both panels no less than 3 inches from the center of the valley trim and no closer than 3 inches to the trim's outer edge. Secure the panels with wood screws as recommended by the manufacturer.