I’m in the midwest, US. I’ve been advised by local advanced beekeepers to run two deep brood boxes and one super. Which I plan to do.
I added a 2nd brood box one week ago and they’ve filled 6 frames with honey. I see no brood in the 2nd box.
Should I have added a super, then added a 2nd brood box as needed? I’m getting mixed opinions.
You did it the correct way. If you add the second deep first, you are looking after the bees. If you add the super first, the bees may not have enough winter stores when you harvest, especially as you should take the super off over winter.
If you put the second deep on first, you may not get a harvest in your first year of beekeeping. However, that is a responsible way to keep bees. In short, you have done the kindest, most responsible thing, well done! You actions will help to ensure that your colony does not starve over winter. 
As we now know that you are a caring, sensible beekeeper do you have a varroa treatment plan yet? 
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Thank you! I was explaining to my husband that if we put a 2nd box on first, before a super, they’ll fill it with what they’ll be living off of during the winter.
So I thought that was the way to do it but I got concerned when I saw no brood. I just want to make sure that’s normal.
We have a local beekeeper helping us for when we need mite or other infestation prevention. We got Russian honeybees from a certified RHBA breeder and he’s been very knowledgeable and helpful!
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If there is a nectar flow on (it sounds like there is a strong one), then the bees will prioritize storage space. When they need to make more bees, they will start clearing honey out of the lower part of the middle frames of the upper brood/deep box, in an arc shape, so that the queen can lay in it. It seems to me that they are happy with the space that she has for laying right now, so you don’t need to worry. It is all normal, and you haven’t done anything wrong.
I’m a new beekeeper and took the advice to add a super on top of my first brood box. For the past week, I’ve had a bad feeling about it. What can i do to rectify the situation at this point? They’re already filling the super with honey. Should I just continue adding supers?
The advice from where?
Do your local beekeepers normally use 2 brood boxes, or leave a super on for the bees over winter? If they use 2 brood boxes, I would buy a second brood box, remove the Flow super and put the second brood box on now.
Beekeeping advice can be very dependent on the region, and I am not familiar with the year-round nectar flow in your climate. If you have a mild climate, with a decent nectar flow for much of the year, you may not need 2 brood boxes.
Here in California, we have long periods with no nectar, because of the dry climate. We still have flowers, they just don’t make enough nectar for the bees. So I use 2 brood boxes to give the bees enough stores to live through the nectar dearths. @JeffH has a climate which produces decent nectar year-round. Hawaii has that too.
I would suggest that you ask a local beekeeping club how many boxes they use for brood, and do the same. The Flow hive is just a different way of harvesting. Everything else about caring for the bees should be the same as your local beekeepers.
I’m in southwest Missouri. Our local feed store has a few beekeepers that I took some advice from. I can’t imagine I’d want to leave the super on over winter, since we do have very cold winters. But then I can’t imagine just one brood box being able to hold and feed my colony over winter, either.
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In the absence of advice from a local beekeeping club (more reliable than advice from one store, or from me!), I would suggest that you buy a second brood box, and put that on. Beekeeping clubs are generally full of people who really care about bees, and know the local conditions. The added benefit is that most are hobbyists and they are not trying to sell you anything.
The Flow super can stay in place for now, as it seems like you have a nectar flow on. Hope that helps. Please keep asking if you need more help.
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