Your bees are smart: by using the top entrance, they save the trouble of having to work their way up through the crowded brood box to get to the storage area for depositing the nectar. I would suggest that you cooperate with them and make it even easier---slide the top super back a bit, making a larger and easy entrance for the field bees all across the top of the brood box. When you see that the honey flow has subsided and traffic has reduced so much that the extra entrance room is no longer necessary and robbing can become a concern, simply slide the super forward again and close up the space. Your smart bees will figure out just what to do and adjust to the new situation by using the original entrances.