yes foam before gravel. but you'll want to cut back fabric foam liner to rocks . for best results or install whats called a bib liner. you cut ruber to fit in the pooling area and around the boulders then foam everything all the joints and edges. Now one trick thats seperates the men from the boys is to let the foam skin over just a little and the take dust / small rocks/ dirt/ wood chunks or what have you and throw it place it push it into the foam what ever works best for you to get the foam covered and have it look More natural once you start playing with it you'll see what i'm talking about . you just don't want such big pieces to cut through the foam and ruin your bond
1" rock or larger maybe needed in the high current areas. some 3/8" in your calmer areas but mixing them up is a must having a pile of 3/8 there only and only one inch there looks un natural.
I would also think about how to make little beach areas for bird baths or other animals.
The liner when folding it up you want to roll it into the pond area or stream and where ever there is a fold and that area in under 2 inches from the top of the fold to the water level you'll want to seal that fold that can be an area that will wick water up and out of the area creating a leak . yes rubber that does not absorb water can suck it up 2 inches or more when in a fold quantum physics.
Your always going to tinker with this sorry but the vidoes of how the pros do it is the best teacher in my eyes. BUT IF YOU START AT THE BOTTOM YOU CAN USE A BUCKET OR a second pump to help figure it out what size pump are you planning ?
From what i see your skills are more then capable of seaming the layout of the falls are coming along nicely. this will give you all you need except the hands and supplies to do it. i would recommend double or triple seaming as the last thing we ever want with big boulders is to be moving and redoing an area because a un for seen .
https://www.gardenpondforum.com/threads/seaming-epdm-liner.26807/
Nice work Sir