You should not use App_GlobalResources or App_LocalResources with MVC. That is because of the way these resources work. These resources are not embedded in your project, but are instead compiled by the ASP.NET runtime. This means that your resources will not be available when not running inside the ASP.NET runtime, which means you would lose the ability to unit test your views and controllers if you use resources in them.
Instead, you should use the approach you mention yourself in your question. Put your resource whereever you want, and set it to 'Embedded resource' and the custom tool should be 'PublicResXFileCodeGenerator'.
Editor, DotNetSpider MVM
Microsoft MVP 2014 [ASP.NET/IIS]