I am not sure I understand your first question:

- if you need to determine which two boxes are connected by a specific arrow, use the Arrow class' Origin and Destination properties.

- if you need two determine whether two boxes are linked in a specific direction and want to find the arrow that links them, use the boxes' IncomingArrows and OutgoingArrows collections, e.g.:

Arrow getLink(Box b1, Box b2)
{
  foreach (Arrow link in b1.OutgoingArrows)
    if (b2.IncomingArrows.Contains(link))
     return link;

  return null;
}