What do you mean by "box at the bottom"? In Aeon Version 2? Maybe a screenshot will help.
Are you used to ATL1 by chance? I ask only because, ATL1's default display of information, with character names at the bottom and the timeline arcs above, with lines going between and setting those little dots or stars to denote birth death or present in the event above, is not possible (yet) in AT2. In ATL2, no matter how many you populate the timeline with, if they are not associated or mentioned with an event(s), you'll not see their name in the timeline. I think you mean that overlay rectangular box that is the small focus of the above timeline, correct? Again, even if your characters are born or die within that box 'view', if there is not a specific event made, and the character has not been associated, the characters remain 'ghosts of the background', so to speak and mix metaphors.
If you want to break down the timeline by characters, maybe use the filter Characters, basically displays events by character arcs, instead of story arcs