The GCS, as i understand this, is not able to config anything without a connected CC3D. The complete configuration is grey, you can't do any changes. When you connect your CC3D, the configuration is filled with the data of your Flight-Controller and you can change the settings on the shown page of configuration. You must save your changes to CC3D before you go to another page or your changes will be lost.
With this in mind, lets look at importing UAV templates or your previously exported UAV-Settings: The uav-file contains the data from more than on or all pages of configuration. When you import all settings in one time, the contents are written directly to your CC3D. After that, the configuration reads your connected CC3D to show the content of the configuration page.
I use 'File->export uav' to make a backup of my settings before i change something. When everything goes wrong i can get my settings back to the CC3D by 'file -> import uav'.
Long post, short answer: You are working directly on a connected CC3D.