When you open the CookieCutter application it looks in your Netscape preferences to find your MagicCookie file. If it doesn't find it you will be given the open file dialog so you can locate a MagicCookie file. Under normal circumstances your MagicCookie file will be found and automatically opened. (If you must be abnormal, you can also drag & drop a MagicCookie file on to the application.)
All domains which have left cookies in your MagicCookie file will be listed. (Note: If none are listed, you don't have any cookies.)
Cookie Cutter maintains three lists. You can change between these lists using the pop-up menu at the top of the window. The lists are as follows:
Current Domains -- The domains which have left Cookies in your MagicCookie file.
Always Remove -- The domains you have assigned to be automatically removed each time you open Cookie Cutter.
Never Remove -- The domains you have assigned to be ignored each time you open Cookie Cutter.
There is a built-in help box which gives you information about what each button does. The best thing to do is open up Cookie Cutter and give it a whirl.