Is there some way to tell CCleaner to keep cookies that come from sites I've bookmarked (in Favorites for IE, Bookmarks for FireFox and Safari) such as by importing all bookmarked sites into the "Cookies to keep" or setting a switch to keep all bookmarked site's cookies?
Its not a possibility. In CC you would need to go to Options>Cookies and select all the sites to keep cookies by moving them into the keep column.
Is there some way to tell CCleaner to keep cookies that come from sites I've bookmarked (in Favorites for IE, Bookmarks for FireFox and Safari) such as by importing all bookmarked sites into the "Cookies to keep" or setting a switch to keep all bookmarked site's cookies?
In IE8, you can set the browser to clear all cookies on exit except those from Favorites; then untick Cookies in CCleaner. I don't know if Firefox and Safari have similar features.