MIDI Through does what it says. It connects your BeBox's MIDI outputs to its MIDI inputs. You can connect both sets of MIDI ports to each other.
The panic button sends all-notes-off messages on all MIDI channels to both MIDI ports. The keyboard shortcut is Alt-Space.
Note: the BeBook states that MIDI input and output #2 do not yet work.
I hate the pseudo-word "thru."