The Directories pane shows a list of directories which will be checked for identical files.
You can add directories by selecting them first in the Directory editbox and then pressing Add to List.

You can refine the search by de-selecting certain folders that you do not want to check. For example, folders that you already did check, or folders that you want to keep as a backup.
Just highlight the folders you want to remove from the list by clicking with your mouse and then select "Remove From List". The folders are NOT deleted! They are only removed from the list.

If you want to run a check on a certain list more than once, then you can save the list with by clicking "Store List". At a later date you can then retrieve the list with "Retrieve List".

You can also clear the complete list and start with step 1 again by clicking "Clear List"