Where should I put the CSS and Javascript code in an HTML webpage?
Put Stylesheets at the Top Links to discussion
While researching performance at Yahoo!, we discovered that moving stylesheets to the document HEAD makes pages appear to be loading faster. This is because putting stylesheets in the HEAD allows the page to render progressively.
Front-end engineers that care about performance want a page to load progressively; that is, we want the browser to display whatever content it has as soon as possible. This is especially important for pages with a lot of content and for users on slower Internet connections. The importance of giving users visual feedback, such as progress indicators, has been well researched and documented. In our case the HTML page is the progress indicator! When the browser loads the page progressively the header, the navigation bar, the logo at the top, etc. all serve as visual feedback for the user who is waiting for the page. This improves the overall user experience.
The problem with putting stylesheets near the bottom of the document is that it prohibits progressive rendering in many browsers, including Internet Explorer. These browsers block rendering to avoid having to redraw elements of the page if their styles change. The user is stuck viewing a blank white page.
The HTML specification clearly states that stylesheets are to be included in the HEAD of the page: "Unlike A, [LINK] may only appear in the HEAD section of a document, although it may appear any number of times." Neither of the alternatives, the blank white screen or flash of unstyled content, are worth the risk. The optimal solution is to follow the HTML specification and load your stylesheets in the document HEAD.
Put Scripts at the Bottom
The problem caused by scripts is that they block parallel downloads. The HTTP/1.1 specification suggests that browsers download no more than two components in parallel per hostname. If you serve your images from multiple hostnames, you can get more than two downloads to occur in parallel. While a script is downloading, however, the browser won't start any other downloads, even on different hostnames.
In some situations it's not easy to move scripts to the bottom. If, for example, the script uses document.write to insert part of the page's content, it can't be moved lower in the page. There might also be scoping issues. In many cases, there are ways to workaround these situations.
An alternative suggestion that often comes up is to use deferred scripts. The DEFER attribute indicates that the script does not contain document.write, and is a clue to browsers that they can continue rendering. Unfortunately, Firefox doesn't support the DEFER attribute. In Internet Explorer, the script may be deferred, but not as much as desired. If a script can be deferred, it can also be moved to the bottom of the page. That will make your web pages load faster.
In my opinion the best practice is to place the CSS file in the header
<head>
<link rel="stylesheet" href="css/layout.css" type="text/css">
</head>
and the Javascript file before the closing </body> tag
<script type="text/javascript" src="script.js"></script>
</body>
Also if you have, like you said two CSS files. The browser would use both. If there were any selectors, ie. .content {} that were the same in both CSS files the browser would overwrite the similar properties of the first one with the second one's properties. If that makes sense.