To flesh this out a bit:
The three timers in the Uno (and similar) are used by analogWrite() to control the PWM outputs on pins 3,5,6,9,10,11.
timer0 is used to implement millis(),micros(),delay().
If you don't use analogWrite() on pins 3,9,10,11 then you can use timers 1 and 2 how you like.
If you don't use the time functions or analogWrite on pins 5,6 you can
user timer0 how you like (but you'll have to inhibit the interrupt handler perhaps).
Timers can be used to just count time (no need to connect to pins like analogWrite() does), or to count inputs (timer1 with pin 5),
or to generate waveforms via PWM, or to generate regular interrupts. Timers 0 and 2 are 8 bit only, timer1 is 16 bit (but can be
configured as 8,9 or 10 bits too).