Hi Grzegorz
I just tried the following on a FRDM-K82F board (using uTasker FlexTimer HAL):
PWM_INTERRUPT_SETUP pwm_setup;
pwm_setup.int_type = PWM_INTERRUPT;
pwm_setup.int_handler = 0;
pwm_setup.pwm_mode = (PWM_EDGE_ALIGNED);
pwm_setup.pwm_frequency = PWM_FREQUENCY(1000, 128);
pwm_setup.pwm_value = _PWM_PERCENT(50, pwm_setup.pwm_frequency);
pwm_setup.pwm_reference = (_TIMER_0 | 0);
fnConfigureInterrupt((void *)&pwm_setup);
pwm_setup.pwm_mode |= (PWM_POLARITY);
pwm_setup.pwm_reference = (_TIMER_0 | 1);
fnConfigureInterrupt((void *)&pwm_setup);
pwm_setup.pwm_mode &= ~(PWM_POLARITY);
pwm_setup.pwm_mode |= (PWM_COMBINED_PHASE_SHIFT);
pwm_setup.pwm_phase_shift = _PWM_PERCENT(25, pwm_setup.pwm_frequency);
pwm_setup.pwm_reference = (_TIMER_0 | 4);
fnConfigureInterrupt((void *)&pwm_setup);
pwm_setup.pwm_mode |= (PWM_POLARITY | PWM_SYS_CLK | PWM_PRESCALER_128);
pwm_setup.pwm_reference = (_TIMER_0 | 5);
fnConfigureInterrupt((void *)&pwm_setup);
It generates 1kHz PWM 50% complimentary signals on PTC1, PTC2 and PTD4, PTD5, whereby the CH0,1 and CH4,5 are 45° phase shifted [binary attached]

This is a snap-shot of the FTM0 registers so that you can compare with yours.
Note that to get complimentary outputs on a channel pair the COMP0 flag needs to be set. Since it is possible to do the non-shifted channels in non-combined mode I have set up the first 2 independently but one phase reversed (using MS_ELS_PWM_LOW_TRUE_PULSES channel setting instead) but could have used combined mode to do the same. CH4/5 (the ones you are interested in) are in combined/complimentary mode.

Regards
Mark