Hmmm, I see.

Well, for those interested, here's the sketch: http://chaos.foxmage.com/canyonthing.jpg
The numbers of course denote layers. Layers 5+6 may also be made into a single layer, I guess, but it wouldn't allow for flowing water.
Both the water and sky should be a bright blue to make a pleasent contrast to the murky colors inside. The background canyon and rocks should be of the same color as the ground, except paler, of course, which would create a sense of depth and close the tileset by showing the player that they are inside such a rock.
Also, I tried to make clear that the rocks ought to have depth. I dislike how many tileset makers just make a texture for the ground, then give it a one or two-pixel border and call it a job well done. Borders with a real sense of depth are harder to do, but should be worth it.

Well, that's just an idea. Either of yours' could work as well.

EDIT: Actually, now that I think about it, the water should be layer 7 for the same reason why the stone spires should be layer 5.