Step by step. You have to have two things to use magic: blue energy (next to your green health bar) and the magic command itself.
You start the game with no magic skills at all. You get your first spell after you first encounter the Hydra boss. If you have already found a lightning symbol and picked it up, then the game tells you that you have acquired Poseidon's Rage magic.
You should have a full bar of blue energy when you get it, and you can immediately test it by doing this: tap right on the D-Pad to select the spell (it's circular lightning logo should be inside the upper left orb), and then you can tap L2 whenever you want to activate it - remember to quickly tap 'O' to dish out more magic damage after you level it up. Each spell you discover is a different D-Pad direction to select it.
If that isn't working (sounds like you did it) be sure you didn't change the controls in the menu. Maybe that messed something up.
