I have done this before with a full size window in the lower wall, (projecting above the top of the lower wall) and an empty opening in the upper wall to form the hole to make the top half of the window visible. You have to keep track of your empty openings if the window moves, but otherwise it should work fine.
An alternative, if you have Door and Window Builder is to make 2 separate windows, the bottom one with no head frame, the top one with no sill (under Setout - Join Adjacent tab (glass joint option as required) )
HTH
Edit: or if you want to use the new-fangled gadgets, do as Dwight suggests.