Every MySQL server/connection supports multiple databases. The most important and needed database is called "mysql", where the server saves it's security, procedures, functions and some configuration information. By default MySQL server allows you to list and see all databases on it (if you have the security privilege to do so, see MySQL Manual Security and also Security Overview). However, MySQL can also be setup to not show it's databases (for security reasons), in which case you need to manually supply your database names. MyCon provides for both situations. To setup your initial connection, first follow the steps in Create a new connection. To change or modify your visible databases select the "Databases" tab on your connection configuration window (after you have tested your connection). If your MySQL server does not allow listing of databases you will notice a "Manual" property just below the Databases in the window. In this case you need to manually and comma delimited specify all the databases which you would like to access and be listed in your folders. By default MySQL does allow listing of databases and in this case you will see the "Visible" property. If you don't select any databases explicitly, all databases shown by the MySQL server will be automatically listed in your Folders. However some servers have a huge number of databases and this might become cumbersome to have them all listed if you don't access 90% of them 100% of the time. In this case you can explicitly specify certain databases to list in your folders, by using the drop down list and checking or unchecking your databases.
Because certain databases may be closed or unavailable after you changed the available list, all open folder panes using this connection, ex. Tables, Queries, etc, will be closed, so be sure to save your work beforehand.