Stopping Serial on RX/TX pins while running Serial on USB
The Serial and Serial1 are two seperated ports. They are not connected. The Serial is the USB serial and does not use pin 0 and 1 at all. The Serial1 is the hardware serial port at pin 0 and 1, but if Serial1 is not used then pin 0 and 1 are normal digital pins that you can use.

Don't be confused by the text labels printed on the board. Pin TX (also called TX1) is D1 and pin RX (also called RX1) is D0.
This is the pinmapping for the Micro: PighiXXX - Micro.

The Arduino Zero uses 'SerialUSB' to indicate the serial port via USB. You can do the same for the Leonardo and the Micro and use the alias 'SerialUSB' in your sketch instead of 'Serial'.
I found it more convenient to use 'SerialUSB' in my sketch, but not many people use it.
The Serial port at pin 0 and 1 is still called 'Serial1'.