Here we go. You have your leg inseams sewn and top-stitched on both legs, and your crotch seam allowances finished (serged or zig-zagged). Sew the crotch seam from back to front with a normal stitch length, stopping at the bottom of the fly panel (where the bottom of the zipper goes). Backstitch there. Lengthen your stitch length to a basting stitch and finish sewing along the lines marked on the pattern to the waist edge. Like so. If you can't see it, the red pin marks where I lengthened my stitch.
Now, press open along the stitching line. (I've said it before, and I'll say it again. . .it is impossible to press too often, so when in doubt, press!)
Then, attach your zipper to your prepared fly shield with a row of stitches. The stitching line doesn't need to be close to the zipper teeth. (On a side note, I suggest you always use a zipper longer than what you need.)
Next, place the zipper (with fly shield attached) face down on your pants front with the edge of zipper tape lined up along the basted seam line. Pin it in place, pinning only through the fly shield and not through the front of the pants.
Flip the front of the pants out of the way and stitch it in place, stitching closer to the zipper teeth this time.
It will look like this.
Now to attach the other side of the zipper tape to the other fly extension. Flip your zipper, fly shield and fly extension combo to the other side, letting it fall where it wants to. Pin the other side of your zipper tape only to the fly extension. Your zipper will be face up.
Stitch it in place close to the zipper teeth.
Now, you are basically done! Flip everything where it is supposed to be. . .it will be obvious. . .and top-stitch. You may want to do bar tacks as well.
Using your seam ripper, remove the basting stitches that hold the fly shut.
You're done! But this part is key. When you sew your waistband on, make sure your zipper is down, and only after sewing the waistband on, cut off the top tails of your zipper.