Every time you create a new site, a default application is created for the new site. So for the website that you currently have, you will see applications "/" (default application) and "Web Application" in configuration at %SystemRoot%\System32.\inetsrv\config\applicationHost.config. You don't have to create a separate application. Deploy your content to the root of the site and you are all set.
Thanks,
Katerina Rohonyan, SDET, Microsoft IIS Team