PIN the zipper between the lining piece and the main pieces. Then BASTE your layers together.
The fabric edge of the zipper should line up with edge of the pocket and flap. The right sides of the pieces of fabrics should be facing each other.
NOTE: The zipper I had was too long and I needed to shorten it. I should have shortened it from the top/open end instead of the bottom/closed end. It worked out OK though.