Special words option is used when you are running comparison by keywords.
This is a list of keywords that are ignored while comparing text by keywords.
If in your job you have some other frequently used keywords then you can edit this list or click "Load special words from file" button to load a text file (.txt) with a list of keywords that Compare Suite should ignore.
The check box on the bottom - "Automatically show keyword tree while comparing by keywords" indicates if Compare Suite show automatically on Keyword Tree window, while comparing by keywords.