The blacklist/whitelist will not really need to be used by probably 90% of users. (personally I don't have any cookies on my blacklist/whitelist)
The blacklist is for flagging individual cookies for removal. say for example you have a favorited website, but there is one cookie (within that favourite) in particular that you don't want to keep. The blacklist allows you to selectively delete that single cookie.
The whitelist is the exact opposite. If you have a website which you would like to keep only one cookie from (and not all of its cookies). rather than favoriting the entire website, you can just whitelist the single cookie. Another useful case for the whitelist is if you have a cookie which is flagged as a tracking cookie, but you want to keep it. For example the "NID" Google cookie is flagged as a tracking cookie, but is needed if you don't want to have to re-log into Gmail every time. (you can whitelist the specific cookie, instead of editing the tracking cookie definitions - which would affect tracking cookies across all domains)
All cookies which aren't favorited are deleted by Cookie, however browsers tend to store references to their cookies in RAM, and these references aren't accurately updated after cookie removes the physical file. This is the case for cache cookies/databases/history. To finalise any removal, it is best to restart your browser.