the super is now honey-less and nicely filled with brood...
Could someone advise me of how to proceed from here? I have two deeps under the super.
Things are better than they can be.
You have a good build up going. The super is free from crytallised honey.
take one high box off. Select from frames those which perhaps have pollen and put them into box. Put the box under brood box.
You have not made (yet) nothiong wrong. Let the build up continues. Take care that hive has enough foor and enjoy your succes.
Many beekeeprs use medium boxes as brood boxes. Nothing wrong in that.