These notes apply to the ​ATMega328P (Uno etc) using the Arduino IDE and libraries unless otherwise noted.

The 328 has 3 timers:

Timer0 (8 bits)

Used for delay(), millis() and micros(). Don't mess with it.

Timer1 (16 bits)

Not normally used. For simple use, see the ​TimerOne library.

Timer2 (8 bits)

Used by e.g. the tone() function.