In Developer Studio, when you create a synonym in the Synonym Editor, it is automatically added to the current project and is visible in the Explorer window.

In App Studio, for a synonym you create in the Metadata canvas to show in the Configured Environments tree, you must select the Show All Files in Associated Paths option in the View Options drop-down menu. The View Options drop-down menu and the Show Files in Associated Paths option are shown in the following image.

Note: If you add a synonym to a project, that synonym will show whether Show All Files in Associated Paths is selected or not.