The Workflow Template that you initially used to create a project is copied as a Project Workflow on the project. At that point, the Project Workflow is a completely separate entity from the original Workflow Template. Any changes you make to the Project Workflow will have no effect on the Workflow Template. This allows you to use a Workflow Template as a starting point and then customize the Project Workflow to the needs of your project. All the features, rules and settings available on Workflow Templates can also be adjusted on the Project Workflow with except for the Project tab that controls project settings when a new project is created from a workflow template.
See the Workflow Templates page to learn more about creating and editing workflows.