We'll start with a coverage area. You can see how it drapes itself over the existing terrain.
When you do, a blue arrow shows up and a ghosted image of a plane.
If you click on the blue arrow, an Elevation value box appears.
You can type in an elevation or drag the arrow up or down to set it graphically.
Then the coverage area becomes flat, at the elevation you've indicated. the sides do some form of tie-in that looks pretty sweet. It's not a simple 3:1 or something like that, it's very rounded and natural looking.
After running the command, you are not stuck with a flat area. You can click on the area again to access it's grips.
And then make adjustments if you want the area to slope.
If you run the Shape Terrain command again, it will flatten the area out once again.
Happy terrain shaping!