It looks like you have steppers (small flagstone) for your edging rock, which is great - very easy to stabilize. HOWEVER stacked steppers are not easy to stabilize... so it's a two edged sword there. You want the edge rock to be resting on the ground - not on top of another rock. You need to start with your edge (the ground level) to be relatively flat. Your liner comes up and over that flat edge and extends behind your edging rock. Place the rock on top of the liner, making sure the rock is level and stable and then pull the liner up behind the rock, folding the edge flat against the back of the rock and then bring your dirt or mulch up against the back of the rock to conceal the liner. It's much easier to see than to explain. Here's a link to the Ponddigger demonstrating various edging approaches:
He's a great teacher and loves to share his knowledge. The whole series on How to Build a Fish Pond is great. This one deal specifically with edging.
Thanks! I'll check it out!