Last Friday at my hive inspection I noticed that my middle position brood box was full. I started my hive here is Colorado with two brood boxes. Then I added a honey super on top. The bees began first filling the top brood box- which I later put the honey super on top of. During my inspection they had not built anything really in the bottom brood box. They also have only filled one frame in the honey super. So…I moved the full brood box to the bottom and put the empty one in the middle, under the honey box. Was this ok? Or did I mess up and possible make my bees mad? Thanks for an help and advice. H th is is my only hive and my first year as a bee keeper!
You are fine having swapped the brood boxes. There is not much point in putting the honey super on unless both boxes are packed with bees.
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Thanks, I’m concerned with it being so late in the season already that they won’t even make enough honey to get themselves through winter
Then take off the super and the empty brood, if they don’t have food in the frames. Winterize your hive (do a sugar roll or alcohol wash varroa mite count, treat if needed, prepare to insulate) and have a plan for feeding them over winter. They are going to need extra food. 
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Thanks, they should still have a couple of months before I need to winterize… stays warm through most of October
Have you done a varroa mite count though? Not just a visual inspection. If not, now is the time to do it to help a smaller colony get through the winter successfully.