only timer0 for millis() indeed.
Then if you use PWM on certain pins, this is where the other timers come into play. that's driven by the atmega 2560 hardware design
- Timer 0 : pins 4 & 13
- Timer 1 : pins 11 & 12
- Timer 2 : pins 9 & 10
- Timer 3 : pins 2, 3 & 5 (16 bits)
- Timer 4 : pins 6, 7 & 8 (16 bits)
- Timer 5 : pins 46, 45 & 44 (16 bits)
other libraries will use some timers (servo, ...)