What is the proper recommended way to add resource files in Web Templates?
Create new "Import SharePoint Solution Package" from Installed templates project and select your web template that you import from sharepoint than add resource file to your solution:
- add Resource File project items to your project. If you do not have to localize code in addition to the markup, you can instead add Global Resources Files.
- Provide a name for the default language resource file.
- Give the localized resource files the same name appended with the language-specific culture ID. For example, MyAppResources.de-DE.resx for German and MyAppResources.ja-JP.resx for Japanese.
- Set the Deployment Type property of each resource file to AppGlobalResource. This causes the resource files to deploy to the App_GlobalResources folder, where they are available to all ASPX pages and controls in the solution. The App_GlobalResources folder is located in C:\inetpub\wwwroot\wss\VirtualDirectories\\App_GlobalResources. Then replace all string in all artifacts(list, modules, pages..) to use your new resource file. For more details check this link.