How to generate 3 PWM signals I have 2560 mega, and I Want to generate 3-phase PWM signal at 62.5khz, synced and shifted 120 degrees apart. 

I need that for 3-phase split-coil boost converter (or even isolated flyback converter), with 3 phase transformer coupled inductor. So I dont need sine wave table like here, but actually, a direct square wave PWM output, from 3 synced digital pins, with chosen duty cycle. How can I do that?
If you have any timers left, I would (regardless of the number of PWM signals and if you need different PWM frequencies) just dedicate a timer to do IRQs to manage them.

The frequency of the IRQs would then depend on how accurately you want to control the duty cycle, ref. also to the comment from Edgar Bonet .