PNG’s support transparency, but Internet Explorer does not (unless all your visitors install a tweak of sorts). So if it’s for web, transparency isn’t a real option.
Having said that, and probably more to your question, I think, drop the opacity in the layers palette.
If you’re talking about transparency in Photoshop and not in Internet Explorer, here’s one way to do it:
(This is my take on it and it works, if there’s a better way then someone please let me know)
1. Load up your destination image (whatever it is that’s going to get the cloud coverage).
2. Load up any grayscale image, doesn’t have to be PNG. It sounds like your image has no transparency in it, it’s just a grayscale image.
3. Select All on the Grayscale image it all and Copy it.
4. In your destination image, open the Channels palette.
5. Create a new empty channel by clicking on the "create new channel" button in the lower right of that palette. The channel will be called Alpha 1.
6. Paste. you should see a black and white icon of the PNG in the Alpha 1 layer.
7. CTRL-click on the Alpha 1 icon. That is, hold down CTRL and click on it. your image should get the "crawling ants" marquee on it.
8. Go to the Layers palette. Click on the your destination layer’s layer, then click on the "Add Layer Mask" button on the bottom of that palette. Your destination image will now have a mask applied based off of the grayscales of your source image. this is the desired effect you want. You can go from there.
9. If the mask is backwards (things that should be transparent are opaque, and vice versa) undo step 8 and hit ctrl-shift-i to invert the mask, then do step 8 again.
You can delete Alpha 1 once this step is done.
~Hanford