How you want to set up your camera for rendering will depend exactly how you want to use the clouds, but I don't know if you were asking about that.
If you disable the atmosphere you can render your clouds on a black background. The alpha channel can be saved from the render view (press 'A' in the Render View to view the alpha channel, then you can save that as a separate image). T-U said the alpha channel can have a chromatic component to it. This means that the alpha isn't always a simple greyscale image in Terragen, because the atmosphere is a bit more complex than that, but for clouds the alpha will be a simple greyscale so there is no problem there. After saving your alpha image, you can convert it to a single alpha channel in Photoshop etc.
Note that if you render clouds this way, they will be premultiplied images (because the RGB fades to black wherever the alpha fades to 0), so you should take care that your game engine knows this. Otherwise you might need to unpremultiply them before using them as textures.
Later, if you want to render a sequence of frames with animated clouds, you can tell Terragen where to save the alpha channel with the "extra output images" filename.
Matt
