Here's a test piece I made:
I sewed the entire seam together first (right sides together) using the biggest straight stitch I could where the zip would go. Rolled and pressed the nylon hem on the back, and pinned the zipper on, centered on the (temporary) seam. Top-stitched through the rolled hems and zipper edge, using a zipper foot. Removed the big stitches with a seam ripper. For a finished piece, I would top-stitch again for two rows of stitches on each side of the zip. If the nylon was hot-cut (or silnylon), and the hem short enough, you could even enclose the hem inside the rows of stitching on each zipper edge, eliminating the rolled hem (which is kind of a pain, esp. on silnylon--hard to get a crease to hold).
For your application, note the zip stops well short of the top of the seam connecting the two pieces of nylon. The reinforcing piece would have a rolled edge, and top-stitch down as Jerry suggests.