Good question. At a physical table, different colored dice (or using tokens to represent Advantage, Disadvantage, or Flat) works well. If you only have a single color of dice, simply put one aside (for the Move die) and use a two-pile system (with Advantage on the left and Disadvantage on the right) to keep track (remember to cancel out Advantage and Disadvantage one-for-one before rolling). Online, rolling a single die automatically means a "Flat" roll. For the other two states, cancel out one-for-one before rolling anything and have the GM (or player) declare whether to take the highest result (Advantage) or the lowest (Disadvantage). On Roll20, Foundry, and Discord (using dice bots), there should also be commands for keeping the highest or lowest results.
All that said, if you come up with another creative approach, please share!