Since you bought a separating zipper, open the zipper almost completely, make sure the tube has the right sides facing each other, and sew both open ends shut. Make sure to center and pin so everything is lining up.
Measure out the squares in the corners so that the bags stand as tall as you want them to.
Cut out the squares on each corner and make them flat and sew together.
Trim the edges so everything looks nice, turn right side out and enjoy!