Why specifically are you wanting to breed your birds?
If the female is dominant to the male and the male is "a little scared of her sometimes" I would not recommend trying to breed these two birds.
The purpose of this forum is to promote only the "best practices" for the health and well-being of budgies.
A big part of responsible and ethical breeding is ensuring you have birds of optimal health and temperament before attempting to breed them.
I recommend you remove the nest box immediately.