Generally speaking, and without being able to see your picture, I would do the following:
- Obtain a picture of a nice sky with clouds. We shall use this in a moment.
- Open you picture, duplicate the background layer, shut off its visibility by clicking on the eye icon, work on the background copy layer
- Use one of the selection tools, e.g. lasso, selection brush, to select the buildings. You will see marching ants once the selection is complete. Then, hit delete on keyboard
- Place the sky picture between the background and backgound copy layers. Use the move tool to position the sky to best advantage.
You can also make your own sky.. Can provide directions for this if you wish
You can add clouds using photo-realistic cloud brushes. Here I used a variety of these brushes. You don't "paint" as you normally do with the Brush tool. Instead just click once to add the cloud. You can find some of these at the Adobe Photoshop Exchange. Enter "clouds" in the Search the Exchange box. An excellent set is the Return to Eden set which I used in this example.
I painted the clouds on a blank layer. To put them behind the lighthouse I copied the lighthouse to a new layer above the clouds layer.