What's happening in the two-queen hive?

What's going on in the new hive? I wish I knew.  I will tell you, though, what I saw when I went in on the 27th.
The day previous, I had seen the bees doing their orientation flights.  I got my net and marker paint and marked 6 bees that were hovering in front of the new hive.  I figured that if I saw any marked bees in the top super, then I would know that the bees I had combined were going out of the hive.  To really make the experiment work I should have marked a couple of hundred bees, but I don't have any grad students working for me.
So here's what I saw, from the top down.  There was loud buzzing going on, almost a roar.  I was surprised by the large number of bees in the Vivaldi box.  Usually there are only a few, but here were a hundred or more.  Many flew off when the lid was removed.  I wondered if they were trying to get out that way, through the vents.

In the medium super I spotted the queen.  But there were no eggs, larvae or capped brood.  There was nectar in many cells.  I didn't see any marked bees.  However, if there's nectar, I have to assume the bees are foraging.  Why isn't the queen laying?  I know she's mated since she was laying while in the nuc.  Perhaps she's being influenced by pheromones from the bottom queen.  I'll have to write to one or two experts about that.  I got the marking paint and marked a bunch of bees.  I'll look for them at the entrance in order to confirm my assumption that they are foraging.  (As of today and a total of maybe 10 minutes of observation, I haven't seen any marked bees.)
In the top deep box, there was still nothing happening.  Only some brace comb on the bottom.
In the brood box, I didn't spot the queen but did see capped brood and larvae. 
The population just doesn't seem to be increasing and there's no honey to speak of, just the nectar in the medium box.  So, the question, what's going on in the new hive?  Time will tell, maybe.

I also looked into the old hive.  There is no honey in the top super and a couple of frames with capped honey in the other medium super.  Lots of brood and several drones.  I did not see the queen.
I brushed bees off the capped brood, collecting almost half a cup for a sugar shake mite count.  The results, 8 mites.  I guess I had ~250 bees, so 3.2 mites/100 bees, an acceptable level.
It doesn't look like a honey crop this fall.

The bees leaving the jar after the sugar shake

The eight varroa mites