To make the flap, I just made the back piece longer than the front piece. I added on enough to cover the top plus a bit more for the part that folds over the front. So if the square at the bottom of the piece is x"by x" and you want to have an overhang of y" on the front, the extra piece at the top of the back should be 2x+y" (plus seam allowance). Here's a diagram:
Note that the flap part is the same width as the piece that becomes the bottom.
I also usually do all my sewing/seaming and leave the end of the flap unsewn so that I can flip the bag through the flap end. Then just tuck the edge up inside and topstitch. For this purse, I made the liner flap longer than the outside flap so that I could fold it up around the outside (the green stripe) and I invisibly stitched it shut. I hope that makes sense!
To clarify: sew the bottom and side seams (just like a jordy) and the corner seams of both the outer bag and the lining. Then sew the lining and outer bag together as follows: put right sides together. Start at a corner of the flap. Sew down the side of the flap, across the side of the purse (don't forget the strap) across the front of the purse, then the other side (strap again) and up the side of the flap. Now flip the bag right side out through the end of the flap. Now turn the edges of the flap inside (and check the length of the flap) and top stitch, or finish as desired.