Yeah it's ugly. Didn't want to say so before.
First take a look at how it should be. The liner is attached under the lip so the water passes over and away from the liner opening.
You are lip-less, so you need to create a way to protect the open part of the liner. Here is what I would do. Not saying it is the only way, just saying it is an option.
1. lay the pond's liner (shown in green) on the spillway area, bunch it up a bit to allow for settling and then glue that baby to the front of the box under the scallop and across the front. (I'd use PL black Roofing sealant.) No bolts, clamps, plates, etc. You are not gluing for waterproof sealing, merely to sorta keep it up for the next step.
2. Completely line the box with another piece of liner (shown in red) and drape it over the other piece about 1-2', then pile on your rocks. Water should not climb 'uphill' between the two liner pieces.
3. I'm guessing the inlet is at the bottom side of the box, correct? You will need to cut a hole in the liner in the box to allow for the inlet. Clean and dry liner and box thoroughly, then run a thin circle of sealant between bulkhead and liner and between liner and box. Then tighten down the bulkhead.
And there is my best idea for keeping the water flowing out and not down between the liner and the box (ie LEAKING).
Good luck!