Edward, I got that part. I just didn't know where to place the new frames with foundation. Do you place them on the outside of the brood chamber or simply swap places?
I use double deeps and a queen excluder so my bottom box is filled with ten frames of brood and pollen above the excluder the food , honey and some pollen is stored.
A more traditional hive set up would bee frames with honey-pollen-brood++++brood,pollen and last honey.
If you use the same size frames throughout the hive I would move the ugly frames up into the supers and pull them out of production after the honey harvest.
When the hive is strong and healthy you can put on new boxes with frames ready for building over the brood nest, also you can divide the brood nest CAREFULLY with a few frames at a time. If you do this to early or in a weak hive they will not bee able to keep the larvae warm and chalk brood can happen.
They build very fast in the brood nest because it is warm and there is an abundance of young bees to sweat out the new wax.
I don't have any fixed places for my frames, it all depends on what the bees are doing with them at the time i check the hive.
If you are in doubt place them outside the brood nest and sooner or later they will get to them.