I normally phase and frequency lock my timer to the zero crossing and use the capture feature of timer2. I filter the capture values to see that the input frequency is within bounds. I calc the time difference between the expected zero crossing and the actual zero crossing and add a correction to my expected zero crossing. I also filter the period of the zero crossing and use this value for my internal timer period - thus my code tracks the frequency and phase locks to the zero crossing input. I add offsets to correct for the phase of the zero crossing input. I use the timer compare to do the cycle timing and firing