Highly reccomend Scott Kelby's lightroom 2 book- it's helped me tremendously.
I don't think you can replace the whole sky, but I was flipping through the book and playing in LR yesterday and discovered something.
If you go to the right side, scroll a little and see where it says color/HSL/greyscale (something like that), click on HSL. Where you see saturation, luminance, etc, look for a little circle at the top left. The "TAT" tool, or targeted adjustment. You click on that, then click on the spot you'd like to edit in your photo. Pull it up or down and you'll see some good changes there. LR will automatically figure out which color you've clicked on and adjust accordingly. Just beware, because if you adjust the blue in the skies it's also going to adjust the other blue areas in your photo. Not too much in my experience.
Hope to have made some sense or helped a bit.
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