ja_4251 on the PGP forums posted a great tutorial on how to get MiJ properly configured (the only error is you need to have L1 & R1 set as buttons 5 & 6, and L2 & R2 set as buttons 7 & 8. Then disable the z-axis): http://pinnaclegameprofiler.com/wiki/index.php?title=Motioninjoy_and_PS3_Controller
Video tutorials after the jump.
Part 1: Getting your PS3 controller working in PGP via MotioninJoy.
Part 2: Creating a PGP profile for SWTOR (You can download my SWTOR profile here).