That sounds absolutely perfect to me! 
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This might be a silly question, but do you just purchase another brood box with frames to use as the ideal box? if so, does the additional brood box come with a lid or the lid should be purchased separately?
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There aren’t any silly questions on this forum! 
If you don’t know the answer, it would be silly not to ask… 
So @Kat11 is referring to an “ideal box” because that is a specific size in Australia. For your climate in South Dakota, you need a “deep Langstroth” box. A second brood box would be exactly the right size for you. You don’t need another “lid”/inner cover/roof etc, as you will be stacking the boxes in one hive. You just have a slightly taller hive, that is all. The extra box and frames are all that you need.
Hope that helps!
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Thank you, Very helpful! I thought we wouldn’t get any honey the first season and would leave the honey for the bees to winter on, should we not even set up the flow frames this summer but use the second brood box after the bees from the NUC fill the first box?
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Very wise to think that. Unlike the Flow advice, I would suggest that you do not use the Flow super in the first season.
The Flow super was developed in a warmer climate than you have, and while it works very well, you may seriously set back your bees if you don’t let them build up their own colony first. Don’t get me wrong, I believe that the Flow hive is wonderful invention. I just think that you need to adapt its use to your specific climate. So for you, that would mean filling 2 brood boxes before adding the super. You might be able to do that this season, but I would aim for next year. Plus you have Varroa mites to deal with, which are not yet a problem in Australia. Make sure you have a plan for controlling them if you would like the greatest chance of your hive making it through winter!
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Ditto to what Dawn said - the first Flow harvest I got was in my 3rd season, when the season/weather lined up well with my strong colony being able to forage consistently and complete waxing of the cells quickly. Now that I’m improving on my varroa management, my winter survivors get an even earlier jump on spring and have been ready for supering by peak nectar flow.
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Hi Kath, I should mention that if your hive smells like your husbands beer brew, you should try to track down the source of the smell. It may not be coming from the area you suspect at all. I think if you remove the honey super for say half a day, then put the roof back on. Then after half a day, remove the roof to see if the fermented odor is still in the hive, as a process of elimination. During that time you can sniff each flow frame to see if you can detect the area the odor is coming from. It could be wafting up from the channels, so check each channel out. Like I said earlier, 3 out of 6 of my channels had fermented honey in them, however the smell didn’t permeate the hive. Others have reported fermented honey in the channels. The only way I knew was the fact that frames were out of the hive, so I could bring the channel opening to my nose, after removing the cap.
My main concern is that the bees don’t like the smell & could abscond on you.
cheers
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Thanks @JeffH, we finally got to 15 degrees today so I’ve taken the top box off quickly and brought it inside. I’ve attached some pics of the uncapped honey which has a very mild smell, and the to box which is sadly very mouldy 
. I’ve cleaned it up a bit and have it out in the sun, but this is from condensation not rain, so I’m not sure how to avoid it.
I should also add there is heaps of capped honey in the other frames. Any tips on what to do with this box?
Hi Kath, well done. I think you should just do what you’re doing, keep it in the sun for a few days & keep it off the hive until the population has built up again. There’s normally plenty of honey in the brood box after an autumn flow, so just monitor that & if you have to feed the bees sugar syrup to keep them going until spring, that’s not a bad thing.
Is there any smell in the brood box now that the honey super has been removed?
The brood box smells ok… But I’ll check again tomorrow. The flow frames do seem to have a bit of a smell, but we might extract a couple frames as we don’t have room in our freezer for them all! I’m hoping the colony is able to keep condensation under control in the brood box, and now they don’t have to worry about all that extra space to keep warm and dry!
I’ll also now get a chance to see if we can crack the frames that had brood in them and if not, I can pull them apart and give them a good clean!
Thanks for your advice and suggestions, much appreciated!
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If you want to kill off the mould, you could spray it with a solution of 10% household chlorine bleach (sodium hypochlorite and unscented) and leave it in the sun. The bleach won’t hurt the bees - they drink swimming pool water, after all! Most of the chlorine will evaporate off in the sun. If you want to rinse it off after about 10 minutes, you could, but you don’t really need to do that. Don’t leave the Flow frames in the sun though, UV degrades the plastic.
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You’re welcome Kath, I use a hive mat, which is a piece of floor vinyl which sits over the frames with a bee space all around it. That prevents any condensation in the roof from affecting the bees. I seem to get more condensation with a week colony than with a strong colony.
I also reduce my entrances during cold weather, which needs doing right now.
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I’ve always been intrigued by the idea of using hive mats instead of inner covers, Jeff - I reckon you get these as scraps from a flooring or hardware store? I might give it a try, seems less cumbersome and could work well as a place to put feed.
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Hi Eva, this is my bee mat video.
I get it from carpet shops. I ask for roll ends. Hardware stores also sell it. One carpet shop did a barter for some honey.
I try to advise flow owners to use a hive mat instead of the crown board because as you can appreciate, the bees propolize the crown board to the honey super, which leaves the roof vulnerable to high winds unless it’s clamped down. With a bee mat instead of a crown board, the bees propolize the roof to the super, negating the need for it to get clamped down.
cheers
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Hi Eva, just want to point out that here in Aus we don’t use inner covers, except with flow hives of course, nor do we use telescoping lids. With our standard lids, migratory, different to your standard migratory lids also, there is a large gap between the hive ceiling and top of frames which is why hive mats are more common here.
Sorry for going off topic, just wanted to clarify.
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So…I’ve been doing a lot of thinking overnight and I thought I would try and return the frames to the hive and build a quilt box. I’ve had the box drying in front of the fireplace and have cleaned up what I can…but there is still a smell in the frames and obviously some mould is growing, but not obvious to the eye.
BUT on a slightly different point…my inner frames as photographed have a rainbow of capped honey above with the inner circle uncapped honey. This is where brood was laid some months ago (definitely worker brood and they didn’t survive as the cells weren’t capped…got to pupae size and that’s the last I saw of them). I’m wondering if I need to do something with these frames while I have them out??? I’ve heard so many different opinions and my gut tells me there’s something not right with these frames now.
I think you should follow your gut feeling. If there is something wrong with the frames that’s causing a fermented smell, regardless what others say, I’d advise to leave them off the hive until you get a chance to clean them up so as to get rid of the smell, because bees don’t like it. I wanted to put “bees don’t like it” in capitals, but I didn’t want you to think I was shouting 
Someone in Sydney recently reported 4 full frames of honey in the brood box. That’s without looking any further. I’d suggest that if you have something similar in your brood box, if you were to insulate the hive for winter, that amount of honey would be sufficient to keep the bees going until spring.