It all depends on the genre, style of graphics and the effect you desire to achieve.
You can get a good RGB value for the ambient and sun by first making them to almost 0, and then slightly pulling them up with heightened blue value. A script creating a panel that shows the current values, bind keys to the sun/ambient and begin slowly to play with the values.
As for the skybox+fog: it's possible and it should work just fine. There should be a fog setting in the WED properties and I think you can change the values with a script.
// fog :
fog_color.red/.green/.blue
camera.fog_start, camera.fog_end
// sun color:
sun_color.red/.green/.blue
// ambient:
ambient_color.red/.green/.blue