Converting individual applications and their settings from GConf to GSettings can be done at will. But desktop-wide settings like font or theme settings often have consumers in multiple modules. Therefore, some consideration has to go into making sure that all users of a setting are converted to GSettings at the same time or that the program responsible for configuring that setting continues to update the value in both places.

It is always a good idea to have a look at how others have handled similar problems before. An examplaric conversion can be found e.g. in the gsettings-tutorial branch of gnome-utils.