There are two ways to create a backup of your database, right click a database in the Enterprise Manager and select Administration & Maintenance | Backup Database: this will open a backup dialog which is different for each database engine. If a backup project for the selected database exists, the dialog will show the settings from the backup project.
Below is an example:
MySQL Backup Database Dialog
Using the OK button will open the Backup Progress screen and gives you the possibility to start running the backup.
The Enterprise Manager also shows "Backup Projects" for particular servers, this functionality can be reached from the toolbar as well.
Enterprise Manager Tools toolbar
Backup projects are useful when you want to store your backup settings and re-use them when running regular backups from within Database Workbench. You can create, alter, delete and execute backup projects from the Backup Project Manager.
The Backup Projects for a registered MySQL server
As you can see, the Backup Project Manager displays the same functionality as the Backup Dialog. The green Execute Backup Project button starts the Backup Progress screen and allows you to create the backup.
For detailed information on database engine specific features: