ENVIRONMENT

The dark queen is Carniolan.  

It sounds like the Italian queen didn't get accepted.  If that's so then there would be nothing for them to make emergency queens from. So I think you need another pair of eyes to look at it.  I'll email you separately from this note to arrange a time.

What to do?

It's time to do an alcohol wash and find out if there is an infestation of varroa since you have more dead bees than there should be. 

If it's not a varroa problem there are more decisions to be made.  Once they've rejected one caged queen the chances of them accepting the next caged queen go way down.  I learned that at last year's state bee convention. 

So it seems to me you have two options (assuming it's not a varroa problem).  One, you can add a frame of bees with eggs and very young larva. They may make their own queen. Secondly, depending on the number of bees in each hive you could merge the two colonies.  

For the newspaper method, you leave the strong colony on the bottom. Put a sheet or two of newspaper on top of the frames in the bottom box. Then put the weaker hive on top.  By time they eat their way through their supposed to be okay together.  

I've got something called a "double screen divider board". Putting that between the two colonies is a bit safer than trusting the newspaper since you are in control of when the merge happens. You can borrow my board.  

You did the right thing asking for help.  See you soon.