johnwasser:
Each of the timers can control two PWM pins. You can certainly use the timers independent of the analogWrite() library to generate a wide range of PWM frequencies. What frequency do you want?
Well not exactly - on the Mega some timers control 3 pins. Here's the mapping I gleaned from the datasheet of ATmega1280/2560:
timer0: pins 4, 13
timer1: pins 11,12 [ and 13 but analogWrite only uses timer0 for this pin ]
timer2: pins 9, 10
timer3: pins 2, 3, 5
timer4: pins 6, 7, 8
timer5: pins 45, 46 [ and 44, but analogWrite doesn't support this pin ]
Double check this though, I might have got something wrong.
millis() etc use timer0, so don't change that one.