Hi, Sandeep,
I think you can use eFlexPWM module to generate the two signal with 90 degree shift, as the eFlexPWM has the function to generate the Phase Shifted PWMs.
I think you can use quadtimer to generate the two signal with 90 degree shift, when one timer is master, the other is slave. But it is easier to use eFlexPWM module.
Hope it can help you
B R
Xiangjun Rong