Huck, in Photoshop, you can play around with each channel. The blues/cyan can be adjusted independently for example. There are several ways to get just the sky darker or lighter without affecting everything else. The easiest is the dodge/burn tool.
Lr is awesome for editing and cataloging a lot of photos. I especially like how you can save and apply presets to multiple images. It saves a lot of time and makes your series of images more consistent, especially working with multiple RAW files. Not as powerful as photoshop, but a lot easier to learn and can do most of the light touch up work.
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