Stick to the low ground and fire charged beam shots directly at the SA-X to destroy it. Your beam must be fully charged to damage it. As it approaches, Space Jump over the SA-X to the other side of the floor while charging your beam, and release the shot when you land.

Stay toward the left side of the room to protect yourself from its jumping attacks, and fire off several missiles diagonally to the sweet spot both before and after it attacks with missiles of its own. Destroy the oncoming missiles with your blaster, and then get yourself into position for your next attack.

When you are fighting the Security Bot, go ALL THE WAY TO THE RIGHT! He can't touch you, you can shoot down his missiles, and if you time it right when he charges at you, you can get 2 hits in with Super Missiles before he attacks again. One hit as he charges at you, then another when he lands after jumping back.

Remember, the X and Metroids are "natural" enemies. In Fusion, the SA-X was willing to die in order to destroy the Metroid lab and an X core willing to blow up BSL along itself. Later, a SA-X "saved" Samus from the Omega Metroid which in reality was just a self-preservation method.