Community Server allows you to insert Javascript in two different parts of your pages: at the top of your page, in the <head> tag, which displays at the top of all of your site’s pages; and at the bottom of your page just before the </body> tag.
Telligent recommends that if you are going to add Javascript to your pages that you insert it at the bottom before the </body> tag.
To add javascript to to the <head> element or the </body> tag of your website, navigate to Control Panel > System Administration > Site Administration > Site Configuration > Setup > General Site Settings.
Click here for more information about the site configuration General Site Settings page.