When you select a volume as the source and destination, CCC copies the entire contents of that volume (minus anything you exclude) to the destination volume, preserving the full hierarchy of folders on the source. If you don't want to preserve that hierarchy, you can back up a specific folder from the source to a specific folder on the destination. In this configuration, CCC will copy the contents of the selected folder to the selected destination folder, without the hierarchy up to that source folder.