The pins 0 and 1 are 5V tolerant. Where did you find that they use a 3.3V logic level? You might be confused about the serial port. The serial port used to access the terminal uses a 3.3V logic level. This serial port is the one next to the Ethernet jack. However, the pins 0 and 1 use a 5V logic level so you can connect them to your Arduino board with no worries. Just make sure the IOREF jumper is set to 5V. This jumper is near the Ethernet jack.