Hello Cyril,
Could you please tell me which example you are using? (KSDK example?, Quick start package example?).
By reading KV5x's reference manual, there is a register for PWM (PWMx_OUTEN) that enable signals for PWMA, PWMB and PWMX modules, once they are enabled, you can configure every port to be used as FLEXPWMx_n, for example, to configure PTE5 to be used as PWM1_A0 output, you should write:
PORTE_PCR5 = PORT_PCR_MUX(5);
previous instruction, let me use PTE5 in its alternative ALT5 mode, which is FLEXPWM1_A0.

I hope this can help you!
Regards,
Isaac