I have an MVC application which is my marketing site and two other regular asp.net applications that I would like to place in subdirectories. Can I use an asp.net app (i.e. mvc marketing) with sub-apps?
Yes! You can. You must define each application as a virtual directory and mark it as an application in IIS. This way, you can run ASP.NET Web Forms and MVC applications side by side, but in different folders.