You can instantiate a differential input or output buffer in your design using the altiobuf megafunction available in the Quartus® II design software. This megafunction allows you to specify your input or output pin as a differential receiver or transmitter and then you need to port both the positive and negative signals to I/O pins. This megafunction is supported beginning with the Stratix® III and Cyclone® III device families.
For more information on the altiobuf megafunction, refer to the I/O Buffer Megafunction (ALTIOBUF) User Guide (PDF).
For Stratix II, Cyclone II, Arria GX, and previous device families, you cannot instantiate a differential buffer in your design. Instead, use the positive leg of the differential pair in your design, and locate that pin in the Assignment Editor. Give that pin an I/O standard assignment with a value of "LVDS" or the differential I/O standard you wish to use. Refer to the device handbook for a complete listing of the supported I/O standards. The negative leg will automatically be assigned to the corresponding complimentary pin by the fitter when you compile your design. This method is supported for all device families that support differential I/O standards such as LVDS.