Cookies are not all bad...they do have uses. :)
Now that we know that, you have two choices regarding clearing unwanted cookies but keeping the good ones you want.
1. Using FF and telling it to clear all history as before EXCEPT cookies which you should uncheck: You could set FF in Settings to NOT accept any cookies and then put your desirable websites cookies in Exceptions.
Firefox > Options > Options > Privacy > Firefox Will: Use Custom Settings For History > Uncheck: Accept Cookies > Uncheck: Accept Third Party Cookies > Click Exceptions and put in the URL's (web address) of the websites you want to keep cookies > Ok. The only thing to watch with this method is if something doesn't work on a particular website that's not in exceptions it's probably because it needs you to accept cookies and you need to add it to exceptions list...can be a pain but you can try it to see if it suits you. Chrome type browsers are better with cookie management because you can instantly click to accept cookies with an icon in the address bar.
Set Firefox to accept all cookies and not clear history > Open Ccleaner > Options > Cookies > Look in the list of Cookies To Delete and move the desirable ones (after you have visited the sites of course) to Cookies To Keep > Ok. Set ccleaner to clear history and anything else you want and then in Options > Settings > Check: Run Ccleaner When Computer starts. Downside of this method is it takes slightly longer for your computer to be ready at start.
Your Choice :)
Point to note in general: if you set a preference with a website your browser can only remember if it retains that site's cookies so you must make it an exception somehow, depending on your browser, when deleting browser data.