Sounds like the right way to change the height of the header to me. First make sure you are editing the verions of that skin in the /Data/Sites/1/skins folder.
Also you should set these to false in Web.config while working on the design, otherwise caching at the server and browser make it difficult to see your changes.
<add key="CacheCssOnServer" value="false" />
<add key="CacheCssInBrowser" value="false" />
otherwise you may need to clear your browser cache as well to see your changes.
The colors will be found in stylecolors.css.
I've actually re-organised the css for the next release as discussed on this thread.
Hope it helps,