GitHub and Visual Studio 2013 Web Application

I’m new to Git/GitHub and I’m struggling to figure out how to use Git/GitHub with a .Net Web Application in Visual Studio 2013.  I’ve got loads of web apps that I need to add to source control.  When I try to add a .Net Web Applicataion to GitHub I get this error message…

…I understand what it’s saying.  But, what it’s saying do and how VS 2013 Web Applications traditionally work with a folder in the Projects folder and a separate folder in the Websites folder.  I don’t know how to make VS 2013 consolidate those two folders into one for GitHub.

I am not familiar with how .NET is structured, but you should be able to initialize git from the root directory that contains your website and project folders. 

Here are a few links on how to do that. Please let me know if these are helpful: