When comparing two directories you can press the Recursive Compare button in the toolbar. This will cause the selected directories to be compared a second time so that more information is provided regarding subdirectories found in the specified directories.
With the recursive option, the Status column will indicate the following regarding listed subdirectories:
Identical: indicates that the contents of this subdirectory are the same between both parent directories
Different: indicates there are differences between the contents of this subdirectory in the parent directories
Source Only: indicates that the subdirectory only exists in the Source (left) directory
Destination Only: indicates that the subdirectory only exists in the Destination (right) directory
If you wish, you may double click on a subdirectory folder. This will open the selected subdirectory in both parent directories for compare. You may press the Parent Directory button to navigate up one level through the directory structure.