Not if you put her on top. That will only perpetuate the situation, imho. A VQ will happily hang out and roam around below, just waiting for the opportunity for a battle royale. Putting the laying queen on top, The exercise would likely end with a bigger hive that still has no laying queen.
The purpose of the arrangement described is least disruptive way to isolate, quarantine, and have the bees ultimately dispatch the possible VQ above. You want the bees moving through the brood-nest of an actively laying queen to get to the entrance/exit. That is why I am recommending she go in the bottom box. Putting the laying queen on top, fewer of the bees will see and know her, more bees will see the VQ.
The alternative is for you to shake all the bees of the main hive through a queen excluder, you find and you pinch the VQ crawling on it, then do the newspaper combine any way you want.
No matter which way you go, you are going to loose bees to the drift back.
I suggest that however you decide to combine them, that you maintain a queen excluder between them for 3 to 4 weeks or until you are absolutely confident there is only one queen present and she is laying and is the one you want to keep around. Whichever comes first.
Pick your preference. Decide. Then just get it done, soon. Not much time left in the calendar for them to have a remote chance of recuperating a brood nest for winter.