I searched a lot online, but I can not yet find how to enable innodb in workbench 6.0. Some search results mentioned changing the my.ini file, but I can not find this file.
Solution: my.cnf (located on the server side - e.g. on Windows localhost, if you are working with WAMP: C:/xampp/mysql/bin/my.cnf) has to be changed:
Putting a # sign before 'skip-innodb' disables this command. Then the restart of mysql will enable InnoDB engine.