Hi! I set up my flow hive 5 weeks ago. They seemed like everything was going fine until this past week. We had some really bad humid days and lots of rain.
May 28th: setup date
June 7th: added the super
June 18th: opened it up for inspection and they looked great.
My friend that gave me the split told me I should put another brood box on top of the original, so I did.
June 26th: I added the 2nd box.
July 6th:
They are filling out the 2nd box
The bees had finally gone up to the super, but weren’t doing anything. I finally figured out that I never turned the key on the frames. I then used the key to turn and checked on them a few days later and there were only a few bees up there. If it matters, Im not sure if I turned the key in the right direction.
July 7th super hot, 90’s and humid
July 8th: torrential rain and humid
I checked on the beehive before the rain came and they were clustered at the entrance of the hive. My friend said they were ok and sometimes do that when it is hot.
July 9th: a lot were dead at the entrance and along with a couple of pupae
July 10th: they seemed back to normal
July 11th: opened up boxes to see what is going on in there, looked fine.
It rained again last night into this morning and when I was taking out the dog, I looked at the entrance to the hive and there were more dead bees!
I need advice!!
How many frames was this split?
You likely added the super way too early, especially if you’re local mentor was recommending a double brood setup. To quote an often posted recommendation by @Dawn_SD:
This sounds like bearding and is very normal on hot and humid days.
They may not have been able to carry away their normal dead and occasional larva or pupa because of the wet weather so they are likely just catching up. A full colony will lose hundred if not thousands of bees a day to normal life expectancy.
When fall comes around you will notice many weak, dying, or dead drones being ejected from the hive. Over winter you will see scattered dead bees in front of the hive and across the snow (which I am assuming you get your fair share of). Scattered dead bees in the winter is a good sign of life inside the colony.
There’s no right and wrong direction, as long as you turn it past straight up or straight down. Use the upper slot to reset the frames and lower slot to harvest.
However, as your bees are still building your second brood box, you should strongly consider removing the super, likely until next spring.
Hello and welcome to the Flow forum! 
The only thing I have to add to @chau06’s excellent response is that you should consider doing a Varroa mite count and inspect the hive for disease on a dry day. Pupae being thrown out of the hive could be Varroa if you have hygienic bees, or it could be chalkbrood if the frames got wet or chilled. For the mite count, please consider a sugar roll or alcohol wash method (use the forum Search tool at the upper right for more info on those) to get an accurate count. Sticky board and direct vision are horribly inaccurate for counting mites. 
Thank you so much for your insight! I am just worried I am doing something wrong.
I didn’t realize there is a upper slot and lower slot for the key…I have watched videos on it and he has just said to put it in and turn, not very clear.
There is condensation also on the inside window, could that be an issue??
Thank you! Although, I def would not know what I am looking for as far as mites🤔what is a sugar roll?
As I mentioned, you can use the forum Search tool (magnifying glass upper right of this screen). This is one of the links that I found using it to search for sugar roll:
Look about 30sec in.
This is pretty normal to see in the morning especially if it’s tiny droplets. This will “burn off” (evaporate) during the course of the morning and the bees will drink some of it up. However, as I mentioned before, you should really consider removing your super until your upper box is completely built out, and by that time, it will probably be time to begin winter prep and remove the super anyway.
Omg, thank you so much, I never saw that video!
I will check the top box in another week and if it is still not full, then I will take the super off. Thank you, your advice is so helpful!!