Google CSE Stylesheet

Question

I have created a search engine for my website using Google Webmaster Tools. Now I'd like to customise the format of results given by the CSE. Google offers me to download the CSS file in whole, but when I attach it to my PHP document inside the head section, nothing happens - the custom style doesn't work.

When I put the Google's style inside the body tag, everything worked normally. But the problem is that this way isn't according to the rules of the World Wide Web Consortium, plus my code gets very "dirty" and untidy if I insert such long CSS code inside the body of my page.

How can I make my external style sheet change the default appearance of the search engine?