"MySQL Workbench is a query and modeling tool and very good at it - the goal is not to perform server tasks - that is server work. You can perform manual backups using Workbench, but I'm guessing is not your long-term goal.
There are many ways you can perform backups. Take a look here for 10 of them. Some of the solutions are OS dependent basically, you have more options if you're on Linux / * nix than on Windows (what's your?). Also, it depends on whether your tables are InnoDB or MyISAM (hope it's InnoDB!).
Two other (Open Source) backup solutions not mentioned in the post above are Percona XtraBackup that can be cron'd or Zmanda's (which was mentioned in High Performance MySQL by Schwartz et al.). Another solution would be MyDumper - again a Percona supported tool (except this one also handles MyISAM tables).
If you are familiar with * nix and file systems, then maybe an LVM solution might be good for you? Try here .
I advise you to study the available solutions and do some tests and see which one suits your needs best. "
* Sometimes you need to get some more! Hug.
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