One of my dislikes about FS2002 was the weather and the way it was displayed. Clouds looked like sheets hanging from the sky they had no depth at all to them I would imagine this has a lot to do with the problem you stated. Any time I tried to use layers the effects were absolutly horriable they were never what you wanted. I managed to find some different cloud textures that helped some what the clouds looked more realistic from a distance but still had no real deapth to them as you flew through them and looked out the window they still looked like sheets. 8)
You might want to consider FS2004 the differance is like noon to midnight . With FS2004 you can set up realistic weather situations that look and act as the real things.
One thing I am curious about though has any one seen a tornado using real world weather in FS2004 I do not fly online And did not know if fs would create a tornado or not.