Question: Can I take the capped supers now and extract then put back on hives? If I do, should they go above or below the supers that I have not extracted?
It is better to extract and give back to hives. Allways put new boxes between brood area and honey.
It seems that 2+2 supers are not enough to your hive. If you have one box capped, you should have 2 supers more under capped box.
You should look, what is going on in deeps. I beleive that they are quite full too honey and capped. It is danger that colonies want to swarm soon if they have not enough room for brood.
If you have 4-5 frame in brood deep honey and pollen, you need third deep. Then lifht full frame supp and put foundations in second box.
I hope that you have in both hive 2 brood boxes.
Tseck how much you have brood. If hive have 1,5 deep full of brood frames your hive will need 5 langstrotm box or 2 L +4-5 medium supers.
If your all brood are in one box, you should need 2 L deep and 3-4 mediums.
When you have good honey flow dont ever let things go so tight that hive is full. Always you need room for new nectar in lowest deep. Otherwise hive swarms and stops working. They store honey into brood area and it not promise good.
So get new boxes and foundations and try more supers.