Occasionally, due to how the script manipulates characters, you may find that some JavaScript you wish to use doesn't work when you put it in the template. To work around this, make it an external javascript. If possible, place all your javascript in the 'javascript header' template, which is listed just below your wrapper at Admin -> Customizations -> Templates. This will be included in every page.

If you want something included more selectively, take the opening and closing tags off and save your script as yourname.js and upload the file to yoururl.com. Then replace that location in the template with <script language="JavaScript" src="http://www.yoururl.com/yourname.js">