To shoot a panorama, you take a series of overlapping images. If you've ever taken a panorama on a sunny day, you've probably seen bands of light and dark running through the final image, the result of your camera's using a different exposure for each shot.
You can't easily fix that problem in an editing program. To prevent it, set your camera to its manual exposure mode and keep the same exposure locked for each photo. Not sure what exposure to use? Point the camera at the brightest and darkest parts of the scene, and note the exposures it recommends--and then set a value in between.