Hosting Website and Web Service as Virtual Directory

I developed a web site, and a web service (using Visual Studio) and testing on my desktop.

Each process has its own web.config file, the web service contains the end-point configuration settings.

I now want to put both website and service on a Server 2012 and have created a virtual directory as follows:

   myWebsite/......(web pages and web.config for website)
         myWebService.....(service.svc and web.config for myWeService)

When I try to edit the mime type for the myWebService virtual directory (add in .svc), I get an error that it can't access the web.config from the parent.  So, obviously I'm not doing something correctly.  What would be a best way to accomplish my goal which is to have the website and myWebService use the same DNS/IP, with external apps calling the service as myWebsite/myWebService/service.svc/....?

Thanks.