FTP is much quicker for multiple changes, but using mamboxplorer means you can do it without leaving your browser. In Joomla, when you edit your "global" configuration settings, the permissions are temporarily modified to enable saving, and then they are immediately reset to 644 for files and 755 for directories (or something like that). Always make sure that these are appropriate settings for the files/directories in question however!
But security goes beyond basic permission setting. It also involves an awareness of to what degree important files are available for the public viewing.
If you have performed a migration by dropping files over the top of an existing mambo installation, you might find that
http://www.mysite.com/configuration.php-dist page can be viewed, and has execution priveleges.
This is no big deal but it helps illustrate how a file and its settings can be overlooked, and if you used it as a backup to your existing configuration.php (on your local machine for instance) or haven't changed the $mosConfig_secret in your global configuration, this info is now fairly easy to obtain.
It isn't necessary provided once you have done your migration so just take it off your online server if you haven't already done so.
Some components allow you make their config files "unwriteable" (e.g. template manager, and other addons) which is great, and if you have finished with a particular item, then i would definately recommend doing that.
This being said, if you need to edit an "unwriteable" file, you may need to use ftp or mamboXplorer to change change the settings back to writeable, but for most maintenance requirements joomla manages the setting of permissions of files and directories very well in of and by itself.
Hope this basic discussion helps make things a little clearer... ?