Oooh, good luck! I'd love to see the finished project!
I think in the dark section you can use a good low carpeting plant, like baby tears or monte carlo. It would almost look like grass. Or you could just use good old dwarf hairgrass, though it would need some trimming. And I guess yeah, some small stones in key parts of the tank would help to keep that illusion of scale.
As for a the "tree" I've seen some people take apart marimo moss balls and spread them on top, making the form of the tree. I personally like the branch you have though, and I don't think you should cover the small detailed branches!
Either way, looks like a great start!