The most imporant things you have to do is to make your freezing rockets charged as much as possible, all the time. Same thing with the beamcanon. Then you have to shoot SA-X with the Missile, jump over her(do not try to damage her/it with your Screw Atack, you will take lots of damage yourself) and shoot her in the back with your Freezing Beam. start rechanrging your weapons as fast as you can after you've fired them. Rinse and repeat, SA-X should go down soo.
I hope you understand what i mean, since it was quite a while ago since i downed her/it and can't really remember the specific name of the attacks.