Rrasco, I think your main concern is hiding the middle wall. I failed to "get that right" on my koi pond, but did better on my goldfish pond, which has a much larger bog. Here are pics of the wall between pond and bog. I used "free" ceramic blocks from neighbor's old garage that got knocked over in a storm (conveniently) the same year I built the goldfish pond. They are stacked on top of the dirt wall, for extra height between the two water areas.
I used one continuous liner for the pond and bog.
Here are a couple of pics of the PVC line run before adding the pea gravel. I use sump pump black flexible water line everywhere in my ponds, except for the PVC in the bogs.
Then added pea gravel, and water. To flush the water out, instead of into the pond, I lowered the outside edge of the bog until the water ran clear, stirring it up some as I rinsed it. Then I raised the outer edge, and watched the clear water flow into the pond. The blocks on the middle wall are laying on the "shelf" of dirt, that's where the rocks will go to hide that part of the liner visible from the pond side.
This morning, I took a couple of pics of the inner wall edge. I'm not good at "drawing" to show how this is done, but from the pond side, I left a ledge about 8" wide to stack rocks on in the water's edge, and then made sure they came up to the top of the wall, where I stacked another rock. This hid the liner from the pond side very well. In this pic, also notice the edge of the liner on the far wall. Do NOT do this! LOL I goofed up and dug too far out, and did not leave enough extra liner. Actually, I think I DID leave enough, but the area has settled, pulling the liner down. That's my story, anyhow.
Addy, see the bog bean plants at the top of this pic? Those are some of them, and part of the reason I had to pull so much penny wart.
Then, once the plants grow, some of them will spill over the edge, like this penny wart. BTW, I pulled about a 55 gal garbage can of this stuff the other day. LOL It sure loves to grow, and is an excellent filtration system for the water, but I did want other plants to survive, too.