Here's how the zipper panel comes together. Pretty standard, really. Some people sew the exterior, the zipper, and the interior together all in one step, but I don't.

Zipper sewn:

Topstitch:

Repeat with the other side and other side's lining.

Now we have a lined zipper panel that's ready to be sewn to the completed gusset. Together, these pieces make up the top, sides, and bottom of the backpack.