I have been working in Capture 1 Pro and LR 2.5 and 3.0(beta). I'm new to pp'ing. I can't seem to figure out how to make significant changes to colors. For example, if a corner of the photograph shows a pure white sky that I want to make dark blue without messing up the rest of the photograph, I can't seem to find any way to accomplish this in either of those tools. Similarly, if I take a portrait of someone wearing a green shirt and I want to make the shirt red (even assuming there is no other green in the picture), I can't seem to do that. I know many of you will think this is too basic a question to bother answering, but I would really appreciate some guidance on how to do this in these tools or alternatively what tool do i need to do this (ps?)? thanks!

If you are new to post-capture processing, instead of trying to get all your basic education from a web forum, you should buy a book or two, or one or more download tutorials and learn the craft systematically. The time and money you put into this will pay big dividends over the longer term. Ben Willmore's Photoshop Stuio Techniques and Latrin Eismann's Creative Digital Darkroom are excellent resources for a well-rounded basic education in post-capture digital imaging. For education focusing particularly on raw image processing and printing workflow, the downloads on this website by Michael and Jeff are very highly recommended.

For what you are describing, PS is a better tool.