If you look at the [ATMega328p datasheet][1] (search for "23.2 Analog Comparator Multiplexed Input") you'll see that you can change the negative pin used by the ADC by setting the ADMUX register. For instance

    ADMUX = _BV(MUX0);

should set ADC1 as the negative input (note that you have to first disable the ADC before you can change this value). What's curious from an Arduino Uno standpoint is that AIN1 is the negative by default which is digital pin 7 on an Uno. I'm not sure how that is handled by the Arduino's analogRead function.

  [1]: http://www.atmel.com/images/atmel-8271-8-bit-avr-microcontroller-atmega48a-48pa-88a-88pa-168a-168pa-328-328p_datasheet_complete.pdf