That is part of the problem. Late in the season to put the super on. It really needs to go on in March when the nectar flow starts, if you have a full hive. If you don’t, you just have to know that you can’t expect a honey harvest in your first season. Plus in MA you are going to need double brood boxes to overwinter - do you have 2 deeps full of bees under your Flow super? Third, you may need to smear some burr comb on the frames to get the bees to accept them. Have you tried that?
Please also search the forum. This question comes up all the time, and there are hundreds of posts addressing various issues, including some really good ones from Flow, especially from @Faroe. 
Like this one: