I would put the flat part in the substrate because it looks too unnatural when it's sticking up. Looks great though
I hear what you're saying...
And, although I may totally fail at this
...the goal I'm going for is to create something similar to the marginal area of a tropical mangrove forest. Here's a decent representation of what I'm trying to pull off:
So, basically the water line will go to right about where the "flat parts" are currently sitting in the tank, with "roots" reaching into the water. I think I have some pretty decent ideas of where to place the plants in the background to fool the eyes into seeing a riverbank in the back of the tank.
We'll see how it actually works when it's all said and done though