When making changes to the fckconfig.js file, you have to remember to reapply those changes in the file when upgrading FCKeditor to a newer version. This could be tedious or you could even not remember this.
To make thinks easier, you can simply use this setting to point the editor to a secondary configuration file that overrides the configurations defined in the default fckconfig.js file. So, you can place that file anywhere outside the FCKeditor installation directory.
You don't need to make a copy of the fckconfig.js file. Just include the configurations you want to change in your file.
FCKConfig.CustomConfigurationsPath = '/myconfig.js' ;
See Method 1 in Configuration File Section for more information.