If they are both strong, why do you want to put them into smaller boxes? I've been doing the opposite and moving from standard national to 14x12.
Anyway, to do what you ask, I'd start off with the smaller box (assuming it contains just foundation) on top. The extra warmth above the brood will help the wax drawers pull out the new frames. This is effectively a Bailey comb exchange. Once several frames are drawn out, I'd swap the boxes around so that the box of new frames is at the bottom. I've found doing this gives the queen more of a chance to lay in the frames before the bees fill them with stores. Then just place the queen excluder between the two, ensuring the queen is in the bottom box.
Others may do it differently, but this approach works for me.
Cheers,
Steve