I often have to integrate applications into pure html websites, maintained with a content creation system. I usually throw the application into a separate folder, and make that folder an application in IIS. I then create a master-page and throw their site’s template in it.
The problem I was having was managing paths to css and images within the template when developing the application using the local file system. I wanted to use all their image resources and the existing scripts and CSS and view all these together when I was developing.