I think that the hand drawn picture at the start of this thread explains the waterflow best, but I will try to make some sense of it using photos.
The terrarium is divided up into three trays. the top two trays (#1 & #2)hold running water and dirt, the bottom tray (#3) holds the aquarium. Tray #2 is also the permanent lid for the aquarium.

I have a large stainless steel container underneath all of this which is hidden inside the bottom of the china cabinet (the bottom three doors in the first picture on page one). Water is pumped up to tray #1 (topmost) by a 800gph pond fountain pump.

The water is pumped up into an empty void underneath the pile of leaves and dirt in the rear left corner of tray #1. It flows towards the front and to the right of the tray under the mossy log.

Continuing past the log it flows again to the back of the tray on the far right hand side where it runs underneath another mound of dirt. Underneath this dirtpile is a 3" pipe which allows the water to go directly into the bottom of the aquarium, completely bypassing tray #2.

This picture isn't actually what the aquarium looks like now, but it does show the pipe very well. Under the rocks I have a screen and a large open area. The water flows up from the pipe, through the rock and up into the area that the fish get to play.

Looking up through the tank at the bottom of tray #2 you can see that the entire tank top is covered except for a small hole which I like to call the lake. On the far left corner you can see a lighter colored area. This is actually part of the stream and water can flow up through that screen.
(the temp tape is not visible when I have the cabinet doors closed, but is easily readable when I open them)

So, the water (most of it) flows up into the lake and then it runs across to the left and then to the back of tray #2. At this point it flows through another screen (which is pretty hard to see in the pic) where it opens up to the top of the waterfall.

This is an old picture taken before the land in tray #2 was installed but it shows how the waterfall ties in. Under the waterfall is another hidden open area with another piece of 3" pipe that drains into the hidden sump. For a biological filter I have used lava rock. I figured that I would never find a rock with more surface area for bacteria than a lava rock and I expect it to work very well. As the water drains into the sump it goes into a large bucket full of lava rock that is inside the sump. The bucket is a little shorter than the sump height and by filling this bucket first I ensure that the lava rocks never dry out, regardless of the overall volume of the water in the sump. Even if the sump gets dangerously low, the bucket will still be full (and overflowing) with water. Also all the land masses are made up of lava rock with window screen on top, then covered with a peatmoss and sand mix.
Reading through this as I proof read it, I see that there are a lot of potentially confusing parts still. I could probably write a much longer description if I were so inclined, but I am not, so I will leave it as is for now. If you have any questions, feel free to ask them and I will try to make things more clear.
As an afterthought, I would say that I am not impressed with the window screen because it tends to let the sand and peat through. I intend to try something with smaller holes in it like a sponge or something similar. It must be permeable because the plants get watered from below the soil instead of the typical watering from above. Also, the water is not restricted to the streams. Much of the water actually flows underneath the land masses.