You choose whether Ebony Fly becomes a creature as the second ability resolves, after you see the result of the die roll. If you don't choose to make it a creature at that time, you can't choose to make it a creature later in the turn unless you activate the ability again.

Players make their choices in turn order and get to know what choices were made before theirs. They may choose an artifact or an enchantment that was already chosen by another player. Once all players have made their choices, the permanents are destroyed simultaneously.