Which Timer can I use on the Arduino/Genuino Micro?
Only Timer0 is used for millis and micros, just as with the Arduino Uno and Mega 2560.

Timer0 is used in "wiring.c".
That same file is used for the Uno, Mega 2560, Leonardo and Micro. The differences for the Leonardo is the pin numbers in "pins_arduino.h".

If you don't use PWM output with analogWrite, then you can use all of the other timers. The timers are set to certain values in the function init (also in wiring.c). But you can ignore that if you never use analogWrite.