MySQL only works with Bukkit/Spigot.
MySQL only is a way to set prefix and sufix (for tab and tag). You can´t do another config with this.
Prefix and sufix in MySQL mode cannot be modified by commands. It will be added in a future update.
A new file called mysqlconfig.yml will be generated. Open that an set MySQLenabled to true. You only need to set info of your MySQL server. I recommend restart the server, but you can also use /tab reload command. Prefix/sufix of your server is now working with MySQL instead config.yml. Enter in your MySQL database and configure that as you want.