I know this is an old post, but I was inspired to go back to this map. Instead of messing around with alpha channels, I decided to focus on layers. It's a bit more time intensive, but I feel more comfortable using the shading of various layers using expand/contract. Each of the different layers is a different depth - the darker it is, obviously, the deeper it is. Here's where I was this morning - I've since added some more rivers and lakes.

map draft 2.jpg