Hi Hesham Desouky,
1. The new method should be added to the generated service. For example, in the generated 'SampleServiceName.svc.cs' file.
2. For NTier application purposes you can download the latest internal build. There we have added a checkbox "Separate the service in a class library". This option will help you to divide the generated files in a separate class library, different from your hosting web project/application. Doing that will help you to separate the layers.
3. In fact there is a code generation template which you may find useful, although it generates proxy objects for plain WCF services. You can find the template and more details about how to use it in this article
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