IIS configuration
Enable Anonymous Authentication status in IIS for the whole site and Windows Authentication for some folder under root directory (for example, /WindowsLogin). In this folder place aspx file (for WebForms project) or create ApiController (for MVC project).
Site setup
On login page add button “Login with Windows/ActiveDirectory account” (in similar way as it is common practice to add buttons Login with Twitter, Facebook, Gmail, etc.). When user presses this button, they will be redirected to the page or controller in /WindowsLogin folder, which require Windows authentication. If site uses some Single Sign-On functionality, locate it in that page or controller, in other case just save Session for Windows users there. If user accessed that page or controller, they had been authenticated as Windows users already.