Each time the Workbench is exited, the Workbench is automatically saved, including all open perspectives and windows. The next time the Workbench is reopened, it will appear exactly as it was when it was last closed.
To exit the Workbench, select File > Exit from the menu bar or close the workbench with the window close button (x). When the latter option is used a prompt will ask if you really wish to exit the workbench.
Note: This dialog also presents an option to turn off the prompting. To turn it back on, open the Preferences dialog and choose the General > Startup and Shutdown preferences page. Check the Confirm exit when closing last window checkbox.