Hey ya Ben. If your queens cells are joined or share a single wall then separating is most difficult or even impossible. I should add the queen is in a protective cocoon, so as long as you don?t pierce the cocoon.
Certain time frames, days old, of a queen cell are very sensitive to movement, even laying a queen cell on its side can harm the queen.
So, you can pic the biggest and sacrifice the other or try to put a queen cell cage on the bottom of each. The latter would take some careful hand work.
For a newbie, you sure have your way with the bees: splitting, queens cells and all. You studied much, listened to the right beeks, so although you may have one year of hands on, your knowledge base is far above a newbie status.
Blessings Phil, to you and FAMILY.
Van