Rendering only clouds: You can turn off enable primary on the atmosphere and any other cloud/haze layers that you don't want to be visible to the camera. They can still affect lighting of everything else if enable secondary is on. On your Sunlight node, turn off visible disc.
Saving alpha channel: You can view the alpha of any render by pressing 'A' in the Render View. You can save the alpha image with the 'Save' button while the alpha is being displayed. Note that the alpha image will contain three channels because some atmospheric components have spectral opacities (Rayleigh scattering), but you can convert to greyscale if you want a simple alpha map.
If you're rendering a sequence, make sure you output "extra output images" - these will be your alpha images.
Matt