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.