Maslord:
The main problem is with timers, when I disable timers_init(), timer0 can do millis(). I do not know how to set timer0 for millis and timer 1,2,3 for PWM! I think this is the first problem.
Why are you trying to do that yourself? Just let the Arduino core do that stuff for you. Stick within the normal framework of an Arduino sketch, which just means not having a function called "main" and you get that with no effort.