Well, I'm a Combustion user myself, so I wouldn't know how AE handles it, but you should be able to set the offset and/or scale in the Z-buffer within AE. That way, you can 'push' the starfield behind the rest of the scene. As for the clouds, they will probably have a transparency channel, so that shouldn't be a problem. I'll try it out and get back to you.

The build is out now!
If you go to e-on's website, click on:
Support->Software updates->Vue4Pro->Get update