Blend Old and New Skies
This is the part where the process gets a little tricky. Choose Select, Inverse from the menu so that everything except the sky is selected, and choose Edit, Copy. You've now preserved the foreground in the clipboard. Next, choose Edit, Paste to add that foreground as a new layer on top of the other two. You won't see anything change in the photo, but the third layer should appear in the Layers palette on the right side of the screen.
Finally, you can introduce the better sky into the photo. In the Layers palette, select the middle layer and then reduce its opacity; the underlying good sky will start to peek through. Adjust the setting until the results look about right to you — it's an art, not a science, so pick a level that looks natural. That's all there is to it.