One one liner panel I first cut a slot for the zipper and a corresponding slot on the pocket. The pocket should be grain side in, so you should line them up flesh side to flesh side, then fold the pocket in half from the bottom up. I lined it up so that the pocket was within 1/4" of the bottom and centered. Now you can unfold the piece and lay both rectangles down and measure for the zipper. Try to make the slot small enough so that only the metal part of the zipper is exposed. Only cut the pocket zipper access slot on the top of the piece.

I used an x-acto knife and shears to cut out the access slots. Then I used the stitching chisel to punch sewing holes up both sides and across the top of the folded pocket. To attach, I turned the liner panel over and used double sided tape to stick the zipper down, then turned it face up to get the alignment right. More double sided tape to attach the zipper to the pocket. Then I used stitching chisels and cut holes through all three layers (panel, zipper tape, and pocket). Then I saddle stitched around to attach zipper and pocket to the panel. That done, I stitched the pocket on three sides (up both sides and across the top). I actually found a video on how to do a pocket and emulated that, but cut down the sewing because if you're using cloth it's easier to do two rows of stitches than it is for leather.

On the other panel, I attached the cell phone pocket. My trick here is to make holes on the pocket, then center it and push the left and right edges in a bit before attaching with tape. Now poke through the holes on the pocket into the panel only on the sides. I sew the two sides, then I use the awl to poke through the bottom holes into the panel, which sort of bunches it up on the bottom as I sew. This gives me a pocket that sticks out a little. Maybe that's overkill. You can decide.

All that done, I laid the pieces face to face and punched holes along both sides and the bottom. Then I sewed the sides and attached the bottom using the awl to punch the holes in the bottom panel. I had to do a bit of bunching to get everything to work. I started by lining up the seams on the panels with the middle of the bottom and sewed from there around from both directions. So four total lines of stitching. This ensured that I kept everything even and the bottom stayed center. I think I even had one stitch lining up the middle of the long side of the bottom with the middles of the panels. I used binder clips to hold things in place. Point is, take your time, work carefully.

Now you have a liner stitched on the outside. If you look inside, the stitches are all invisible, which was the point of doing the liner this way. We'll do a similar thing on the outside, but then turn the bag inside out to hide the stitches.