Hey Stephen,
for not so experienced devs I think it is better to use one of the GUI tools we wrote to do tasks like dumps or other maintenance. See
http://dev.mysql.com/downloads/gui-tools/5.0.html, where you can download a package for your platform (if supported). Once installed start MySQL Administrator, create a connection to your database server and go to the backup section. There you can easily select a schema or even a number of objects in different schemas and let them write into an SQL script, which then can be reverse engineered by MySQL Workbench.
You can then do your changes and use the dump you created in the first step to let WB create a new script that only contains the DDL for things that have changed. You can use MySQL Query Browser to execute this script (QB can be started directly from MA and vice versa, using the same db connection).
Mike
Mike Lischke, MySQL Developer Tools
Oracle Corporation
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