ahh...I call a super something that is idealistically desired to hold honey, ie a honey super and that which is preferred for brood, a brood box. so when you mentioned super I had thought you already had your second brood chamber, and were now about to add a box to accumulate honey.
I like to move my brood down personally, ie put the box under the first one when starting a hive, but different people do it different ways, like everything else in beekeeping, haha. some people also go with a deep and two mediums and keep the deep in the middle and the mediums on the top and bottom and then switch them. some go with just three mediums, or two deeps, and some go with jumbo's (I do deeps and jumbo's personally)
So in short, either way is fine, but I go under. and only after both your brood chambers are full then you add a honey super...when that is full, or close then my last response applies.