When adding a second brood super which has new foundation do you put it on top or under the first one?
May I answering with another question?
Where put the bees their honey? Or in what side -top or down- put the brood?
Let`s go and think (use your mind). First: always the bees put honey up and brood down. In a natural cave, the combs are built from up to down. Never have honey below brood.
Conclusion: if you add a brood box, put under.
-if you add a honey box, put in on top.