The serial communication over the USB connection also appears on pins 0 and 1 and it is best not to use them for anything else unless you know exactly what you are doing.
You have not told us what Arduino you are using. An Uno only has one hardware serial port (pins 0 and 1) but you can use SoftwareSerial to create a second port on other pins. A Mega has 3 spare hardware serial ports and a Leonardo or Micro has 1 spare.
On an Uno (or any Arduino) the analog pins can also be used as regular digital I/O pins.
The Mega also has a lot more I/O pins if that what you need.