STM32F PWM phase shift

Counter mode to Center-aligned mode 3 (CMS[1:0]=11 in TIM1_CR1). And then use PWM mode 1 for TIM1_CH1 (OC1M = 0110 in TIM1_CCMR1) and PWM mode 2 for TIM1_CH2 (OC2M = 0111). Now they'll share the same frequency and if you use the same pulse length in TIM1_CCR1 and TIM1_CCR2 they´ll have the same duty cycle as well.

    TIM_TimeBaseStructure.TIM_Prescaler = 0;
    TIM_TimeBaseStructure.TIM_CounterMode = TIM_CounterMode_CenterAligned3;
    TIM_TimeBaseStructure.TIM_Period = TimerPeriod;
    TIM_TimeBaseStructure.TIM_ClockDivision = 0;
    TIM_TimeBaseStructure.TIM_RepetitionCounter = 0;
    
    TIM_TimeBaseInit(TIM1, &TIM_TimeBaseStructure);
    
    TIM_OCInitStructure.TIM_OCMode = TIM_OCMode_PWM1;
    TIM_OCInitStructure.TIM_OutputState = TIM_OutputState_Enable;
    TIM_OCInitStructure.TIM_OutputNState = TIM_OutputNState_Enable;
    TIM_OCInitStructure.TIM_Pulse = Channel1Pulse;
    TIM_OCInitStructure.TIM_OCPolarity = TIM_OCPolarity_High;
    TIM_OCInitStructure.TIM_OCNPolarity = TIM_OCNPolarity_Low;
    TIM_OCInitStructure.TIM_OCIdleState = TIM_OCIdleState_Reset;
    TIM_OCInitStructure.TIM_OCNIdleState = TIM_OCIdleState_Reset;
    
    TIM_OC1Init(TIM1, &TIM_OCInitStructure);
    
    TIM_OCInitStructure.TIM_OCMode = TIM_OCMode_PWM2;
    TIM_OCInitStructure.TIM_Pulse = Channel2Pulse;
    
    TIM_OC2Init(TIM1, &TIM_OCInitStructure);