I'm probably doing this all wrong, but I've been moving most of the filled nectar frames to the far outsides, and putting empty comb/foundation on each side of the brood nest which I basically leave alone and in order.
The brood frames usually have a circle of nectar/pollen surrounding the brood, and the empty combs give the queen somewhere else to lay. If there's a partial nectar frame (like brood on one side & nectar on the other), I leave it right where it is. My understanding is that you generally don't mess with the brood nest order.