The way to do this is to make sure you shoot in Manual mode at equal exposure, then when you do Merge to panorama, you should select “vignette correction” in Photoshop. This will create fine panoramas without any strange blobs in the skies. If you didn’t use manual exposure on your camera, select all the images in the filmstrip in Develop and select “match total exposures” from the Settings menu. If this doesn’t fix it, you need more sophisticated panorama tools than Photoshop. I use hugin, which does exposure and white balance correction as well as complex lens vignette correction if you need it, but it has a very steep learning curve. Other more friendly tools include things like PTGui and many others.
