The clouds are all photoshop.
Make yourself a cloud however which way you want on a transparent background. Copy it, paste it on a new layer below the cloud but make it black by darkening it. Save the file as a PNG.
Next bring it into construct through use of a sprite. Then go to opacity of the could sprite and put it at 50 or whatever looks good to your eye.
Add a bullet behaviour which ever direction you want and BANG. Got yourself some top down clouds.