If you have an overhead project with multiple phases and want to use only one project for entering overhead time, you can choose to keep the parent project active and change the status of the phases to Inactive or Completed. This can be done in the Projects > General > Details screen. After you change the status of the phases, they are no longer listed in the Time Entries drop-downs and only the parent project is available for entering time.
You can also merge the projects into one. Check Core Help Center for details on that.