After creating a new project using ASP.NET MVC 5 Empty Project, you can right click on the project, then click Add.. > New Scaffolded Item..., select MVC on the left, then MVC 5 Dependencies and choose Full dependencies from the prompt.
This will add a default layout (Views\Shared\_Layout.cshtml), Content folder, Scripts folder with bootstrap, jquery, modernizr, etc, and other things the Web Application template creates.
If you get the error “CS0103: The name ‘Styles’ does not exist in the current context” just add <add namespace="System.Web.Optimization"/> under <namespaces> in Views/web.config