Nick Grattan has a great post about the location of the SharePoint 2010 Global Resource File Locations. 

:\\VirtualDirectories\\App_GlobalResources C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\14\Resources C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\14\CONFIG\Resources

And how they are used:

• Resources files in App_GlobalResources are used when code in an ASPX page refers to a resource, e.g.
  
• Resources files in the Resources folder are used when referencing resources using the SharePoint object model, e.g.

btnExport.Text = SPUtility.GetLocalizedString("$Resources:GlobalSiteResources, Tab_Export", "GloablSiteResources", language);

• Resources files in the Config/Resources are copied into the App_GlobalResources folder whenever a new web application is created. By adding the resx files here you will ensure your application will be able to access its global resource files in new web applications.