Is the Atlassian site built using Confluence?
Atlassian use Confluence for parts of their site but not all. Much of the customisation of sites is achieved through the Theme Builder Plugin which allows you to edit Spaces and the entire instance extensively through a simple WYSIWIG editing tool. It also allows you to create standard layouts and more advanced effects are achieved using CSS. You can use Confluence’s layouts to change the layout of the site, add logos and banners, move or change the appearance of menus, and control the display of pages and blog posts.