At the bottom of each story there are links to "Add to favorites" or "++Bookmark". "++" means "add". Click a link to add to either list.
Bookmarks and Favorites are two different things. Favorites show up on your My Account page, and there's a tab there to bring up your Bookmarks.
To remove something from Favorites, go to the story itself and down at the bottom is a link "remove from favorites". Similarly, if you have used ++Bookmark to bookmark something, there should be a link at the bottom of the story that says Bookmarked, click it to change it back to ++Bookmark and remove it from the bookmarks.
For Bookmarks, there should also be a link in the right column menu under your username that says My Bookmarks where you can manage them.
Why both? Well, we started with favorites, then added bookmarks which had more options and easier to manage but no one wanted to give up their old favorites list. :)
It's kind of nice to have two different lists, I use favorites for things I want to re-read and the book pages of serials and bookmarks for things I haven't finished reading or haven't gotten around to reading.