InstallShield MVC2 Application deployment on IIS

I want to be able to deploy a MVC2 application as a web application on IIS using the installshield. When I try开发者_StackOverflow to deploy the application it just simple copies the whole solution to IIS instead of converting it to a web application. I created an MSI using VS2010 which converts the code into web application and then called that through installshield installer (which basically does some other stuff as well). But it creates two references in installed programs visible through Add/Remove Programs which in turn makes me uninstall both in order to completely remove the application. Any suggestions on how to go about at this?