So after reading a million threads and trying to figure out the best approach on how to add the boxes I ultimately went with @Dawn_SD method and put the new box on the bottom.
I opened up the hive and there were bees on all frames and the first frame I pulled on the end had EPI-PENNY on it which was cool to see her laying all over the place. I have attached pictures of a few of the frames that were in my first box.
Only one issue and I am a dumbass because I didn’t think through this when I added the box below. I set the new box below then set the first box on top but forgot about the comb they built on the bottom. It was on thred frames. So I let it settle in and pushed the three frames lightly down so the top cover could be added back on.
Now I will cross my fingers and hope for the best. I will open it up and check it in a few weeks. 
