Hello all…I am setting up a new hive outside Pittsburgh PA. I am going to have two brood boxes and a flow super box. I know that the first brood box needs to have bees on all of the frames before adding the next box, but what order should I add the boxes. Should I add the second brood box, then the flow or should I add the flow and then the second brood box. I kept bees almost 40 years ago and much has changed since then. Thank you for any help
Hello and welcome. @Eva is in the same state as you. 
Fill the second brood box before adding the Flow super. You will have a stronger hive that is more likely to make it through winter. Be ready to treat for varroa too. It probably wasn’t such a nuisance 40 years ago as it is now. 
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You should add the second brood box only when the ‘in use’ brood box is crowded with bees and needing the extra space. When you are ready to add the flow super throw away the plastic queen excluder that came with the kit and but one of either stainless or galvanized wire. The plastic queen excluder sags in summer heat and becomes brittle in winter and easily breaks any time as you remove it for brood inspections. A metal one will last a lifetime.
Cheers
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Dawn & Peter, thank you for your input. Where can I buy a queen excluder that you are talking about. The flow hive is not as wide as a standard hive. I looked at the honeyflow.com website and all they have is the plastic one. Thank you all for your help!
I like this one:
https://www.kelleybees.com/wood-bound-queen-excluder-8.html
It may be a little wider than the hive boxes, but not enough to notice once it is in place.
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As Dawn has said, if you have either the 8 frame flow hive or 8 frame Langstroth any bee keeping will have metal queen excluders in stock. Above that you fit the flow hive super.
Cheers