During the game, the Fullmetal Alchemist is taken over in main control, other words, you can only control Edward. However, Alphonse can be controlled indirectly, via four simple commands.

Call : R1 When He is away from Ed, Al will move towards Ed.
Tackle : R1 When He is near Ed, Al will tackle enemies.
Use : R1 When you are near a weapon, Al will use that weapon.
Special : R1 When your Alchemy Gauge is fully charged when Al is near Ed.