The queen won't generally cross a frame of honey to lay worker brood. She will to lay drone brood.
So if you have brood in the supers with honey, put all of the brood in one, and honey in the other, and then put the honey above. As the brood hatches they will start filling the cells with honey.
I haven't used excluders, and they will usually start out in the super, raise brood there, and then as they move down and start storing in the spring they will fill it up with honey as the brood hatches, and then I can safely put supers on.
Some people won't extract out of any comb that has had brood raised in it(dark comb), but I do and don't have a problem with it.
If you have drone comb from foundationless frames in the supers, you will need to keep an eye on that.
Rick