My new packaged bee colony has thrived and filled out at least 8 of 10 frames. Good brood production and some honey stores around the periphery of the frames. Last week I added my Flow super but after further inquiry, believe I should be adding a second brood box, as I live in Massachusetts (Cape Cod) and want to make sure that my colony is strong and has winter reserves. My question pertains to how I should go about this. I assume I should add a bee escape to remove bees from the Flow super and then add the brood box on top or bottom of the first brood box? What do I do with the flow super where there has been a weeks worth of activity? Should I just plastic wrap it until I am ready to put it back on? Should I clean it and start fresh? I want it to be safe, ready to go and attractive to my bees when the time comes. THANKS for your input.
Hello and welcome to the Flow forum! 
You probably don’t need to add a bee escape, but you could try it. I would just add the second brood box on top of the first, put the inner cover on top of that. If there is any honey in the Flow super, you could put it on top of the inner cover, and the bees should move it down into the new brood box. Bees often treat boxes above the inner cover as being “outside” the hive, and they like to have all of their resources close to each other (honey, bee bread, brood etc).
If there is no nectar in the Flow super, just take it off the hive and leave it some distance away until evening. All the bees on it should have returned to the hive at that point. I would then freeze the plastic frames for 24 hours to kill off wax moth and small hive beetle eggs and larvae, then wrap closely in burlap an store in a cool dark place (like a garage) until next season when both brood boxes are almost full. Don’t clean the frames. The bees will have put footprint pheromones and probably wax on the cells, making it smell like home. That will make them faster to use it next year. 
That great advice. And I would be very reluctant to clean the frames. What if there is a small amount of nectar in the flow frames?
As long as the bees can be persuaded to abandon the frames, just proceed with the freeze and storage. I have stored frames of honey in the freezer over winter on occasion, but it is not desirable, given the space they take up and the need to keep them upright to stop the honey from dripping out slowly into your nice clean freezer…
You can also crack the frames open on the hive if you want to. The small amount of honey should drain out, and the bees can’t store more if the cells are open.
Thank you so much for your support. I removed the Flow frames and put them in the freezer.
OK Thank you. I followed your suggestions I added a second brood box with waxed foundation and moved a couple of brood frames into its center. I also added some sugar water in a feeder in lieu of a 10th frame. Probably didn’t need to but wanted the 2nd brood box to be inviting. A couple of days later, I went away for a week and returned to some pretty rainy weather. So I wasn’t disturbed by a relative lack of activity. Yesterday I did a hive inspection and am now quite concerned. First, I didn’t find the queen, who was well marked. Second, I didn’t see any activity on the new frames although there was activity on the two frames that I moved up to the second box. Last, I saw what looks like a lot of dead, larvae, some looking pretty dried up. Photos are from the main brood. There seems to be reduced stores as well. Not sure what to do next. I have queens available next week from our county beekeepers association. But is something else wrong?
Thank you for the feedback and photos. Very helpful!
That alone doesn’t worry me. Queens are by nature VERY elusive! Even when marked, they are expert at hiding. Believe me, I have spent many hundreds of hours searching for queens when I really, really needed to find them!
What does concern me a little more is the brood pattern on your photos. There is capped brood, bee bread and some honey. All of that is fine. However, I don’t see any eggs or uncapped larvae. Is your queen excluder still in place? If so, you should remove it ASAP. It goes below a super, but never between brood boxes. You probably already know that, but many people are not aware of this.
That sounds suspiciously like chalk brood. Chalk brood is a fungal infection which often starts after brood has been chilled from a long inspection on a cold day, prolonged cold rainy weather, or in a hive which has too much space for the bees to heat. Is there any chance that you could get a local experienced beekeeper to take a look with you? Not much to do about it, except reduce the hive size and let the colony strengthen itself with food and numbers, if it is just too much space for now.
That may be an option, but a better option (if you can get access) is to buy a frame of Brood In All Stages (BIAS) from a club member. This should have capped and uncapped brood, with preferably some eggs. If your hive is truly queenless, the bees will make a new queen from the eggs or very young uncapped larvae. They are far more likely to accept this queen than a mated queen, but both methods can work. It does take longer to let the bees make their own queen though, so you will need to judge how strong the colony is in terms of numbers of bees.
I am sure I have missed something, and perhaps I can get @Eva and @JeffH to add from their experience. Beekeeping is tricky, but you are asking good questions. Please keep asking and we will try to help
Hi & thank you Dawn. I’m not seeing any young brood in those photos either, however in the second photo the bees have purposely left an area empty of fresh honey, which indicates to me that they left that area empty for the queen to lay in. Because there is no emergency queen cells, with the presence of healthy sealed brood in the bottom photo, indicates to me that there must be a queen in the hive. I agree that they can be hard to spot, especially when you need to & time is limited. I like the suggestion of the addition of the frame of BIAS. It can be used as a test frame. I also agree on the suggestion of chalk brood.