The deeper water / darker blue is a lower layer than shallow water. Since your lake is currently comprised of shallow water, if you place deep water on top it gets moved to the "deeper water" layer, which is under the shallow water.
When I create a lake with a river attached to the coast, I use the coast line tool to create the river and the lake - which makes the river and the lake in deep water blue. I then create the shallow water outline and place it along the coast, down the river to the lake - whch can now show shallow and deep water.
I know that's a tough work-around, but that's what I was forced to do to accomplish a lake with shallow and deep water showing.
Someone more adept at CC3 might be able to give you a better answer. Sorry not much help!