they will (usually) move to the top and build down again....however, if there is honey over the brood in the 1st box, the queen may not move up to lay. it is their natural inclination to store honey above the brood, so you may end up with a 2nd box full of honey rather than more space for the queen to lay.
by putting the 2nd box under, you do not need to worry about honey being over the existing brood, and it is less likely that they will use the second box only for honey storage.
you can pull some brood from the bottom to the top and replace those frames with foundation. this will encourage them to move up and it will give the queen room if that is your goal.
because you have added the 2nd box so late, and brood production will probably decrease soon, you will need to check that 2nd box before winter. if it is not used, you'll want to remove it.