Hello.
You can program the registers directly.
1st. Configure the Processor Expert PWM.
2on. After Processor Expert Initialitzation "PE_low_level_init();", set this code:
FTM0_MODE |= 1<<2; // Write Protection Disable (1)
FTM0_SC |= 1<<5; // Center Aligned PWM CPWMS=1
FTM0_MODE &= 1<<2; // Write Protection Enable (0)
This code works for me on K22.
Change FTMx to used Timer.
Regards.