It is possible to change the serial port that the Maestro uses. Are you using the Basic.ino file in the PololuMaestro library as an example? The SERIAL_PORT_HARDWARE_OPEN object in line 29 is an Arduino serial object that points to the first open Serial port on the Arduino. You could change line 29 to:
#define maestroSerial serial2
This would use the TX2 and RX2 pins on the Arduino Mega 2560.