The contents of your favorites box are your current "my marquee" selections. You can have up to ten links in "my marquee" at one time. If you surpass ten links, the extra links will be placed in the "stored links" box for future use.
To organize/modify your favorites, use the "add" and "store" buttons to choose your top ten favorite links for "my marquee." Then click "save all changes" to complete this process.