I answered a similar question on choosing a color scheme. In addition to that answer, to answer your question about what should have color impact, you should give special emphasis to elements that matter to the user and what they're trying to accomplish. Keep in mind, however, that color shouldn't be the sole way that this is indicated. Accessibility for color blind users is important and so size, text, whitespace, and shape all play a role as well.

I answered a similar question on choosing a color scheme. In addition to that answer, to answer your question about what should have color impact, you should give special emphasis to elements that matter to the user and what they're trying to accomplish. Keep in mind, however, that color shouldn't be the sole way that this is indicated. Accessibility for color blind users is important and so size, text, whitespace, and shape all play a role as well.