*"how do you line up the screw holes from the pocket on the back side of
the door panel?"*

- tape a piece of paper on the pocket, draw around it, punch holes on the
screw holes then take the paper out and tape it on the door panel and drill
holes - You don't need to take out the whole door panel, just remove  the
clips on the bottom and left side of the panel (facing it)

or

- take a piece of chalk, carve it till it's small enough to be inserted in
the screws holes - a piece of chalk for each screw hole. Position the
pocket with the chalk over the door panel and then you will have chalk mark
on it, it's where you will drill the holes.

remember to give clearance for the glove box.