Whenever i create a website, i like to try my best to create a consistent look and feel for the entire site as much as possible. If you change UI elements such as navigation links when you go to an installed web application on your site you WILL confuse your users.
That said, it isn’t always practical to shoehorn your entire main site design in to an application without downgrading that applications functionality. With phpBB for example, if I wanted to use the Iswapyou main site design I would need to have two navigation bars (the main site nav and phpBB’s nav) on every phpBB page. This would take up too much space on the page and introduce more clutter than i wanted to, so I instead put my iswapyou main sites navigation links into phpBB’s navigation bar.
