But then you'll have 2 atmospheres. Here's what I do:
Surface the planet normally.
Add a sphere object.
Put it at the same place as the center of the planet. This should be x0 y-6.378e+006 z0.
Change the radius to 6.378e+006. Now it's the same size as your planet. On the "Surface Shaders" tab click the button next to where it says "Default shader 01". Go to Create new shader and under Other surface shader click Water shader. Now you have a sphere of water around your planet.