In the file AdapterScenarioFullSafe2003SubClasses.config, which comes with the extended entity templates for adapter, and which drives the class generation, you have to create a new TaskGroup, like the "Database Specific Project tasks" taskgroup.
In there, you place the extended class generation tasks (move them from the other group). Remove the tasks you don't need, though keep the VS.NET project task, which generates a vs.net project for you if it's not there. You then get your extended classes in a separate vs.net project.