You may only use one specific Element per round, yes. That means your three decks can use all the 12 Elements, but none of the decks may use an Element the other decks use.
For instance, deck 1: Fire/Light/Life/Water
Deck 2: Aether/Gravity/Time/Darkness
Deck 3: Death/Earth/Air/Entropy
That's legal. Using three monodecks works as well. As long as you don't use the same Element in two duels during the same round, you're good.