Hey LT2D3D,
I'm in the same boat as you. been learning and rendering clouds with Terragen2 all week in hopes of creating elements for a matte painter, cyclorama, etc.
Switching off the atmosphere is key, as you've already found.
What software are you loading up the renders?
If I load up the colour and alpha in Nuke, and merge over another plate, it merges perfectly, as Nuke assumes the render is premultiplied by default. If you're getting black edges, like Matt says, you may need to unpremultiply the image. (divide the rgb by alpha).
cheers,
Jordan