MSP430F5438 - ADC Setup Verify

I am attempting to use the ADC on my mspf5438 to trigger an LED at this point and later on a initiate UART communication.  For now though I am trying to just light the LED.  I am using the following code but the input voltage seems to be different than what I'm actually getting from conversions.  My input is a sine wave with a changing peak to peak value.  It has an average value of 2.1V.  I want to use an externally supplied Vref+ of 3.3V and Vref- of 0V, which I have supplied to pins 9 and 10 of the MSP430.  My input to the ADC is denoted as P6.5/A5, which is pin 2 on the msp.  My LED is connected to P6.1/A1, pin 98.  I have a few specific questions in addition to asking someone to review my code.

1. Do I need to enable pins 9 and 10 for the reference voltage as inputs in addition to supplying the voltage?

2. If I set a state for a specific port, such as P6OUT |= 0X02, does it only affect the pins which I have configured as outputs?

/////////////////////ADC Setup//////////////////////////////
  ADC12CTL0 = ADC12SHT02 + ADC12ON + ADC12REFON;       // Sampling time, ADC12 on
  ADC12CTL1 = ADC12SHP;                                                                  // Use sampling timer
  ADC12IE = 0x01;                                                                                     // Enable interrupt
 
  ADC12CTL0 |= ADC12ENC;
 
  P6SEL |= 0x20;                            // P6.5 ADC option select
  P6DIR |= 0x02;                            // P6.1 output for LED X1
  P6OUT = 0x00;                            //Start LED in off state

while(1)                                     //Continuous conversions?
  {
    ADC12CTL0 |= ADC12SC;                   // Start sampling/conversion
       
    __bis_SR_register(LPM0_bits + GIE);     // LPM0, ADC12_ISR will force exit
    __no_operation();                                         // For debugger
  }
 
}                //End of main()
 

#pragma vector = ADC12_VECTOR
__interrupt void ADC12_ISR(void)
{
 

  switch(__even_in_range(ADC12IV,34))
  {
  case  0: break;                           // Vector  0:  No interrupt
  case  2: break;                           // Vector  2:  ADC overflow
  case  4: break;                           // Vector  4:  ADC timing overflow
  case  6:                                       // Vector  6:  ADC12IFG0
  
    last_state = ADC12MEM0;                 //This little bit of code lets me
    if(last_state > new_state)                  //store my highest value converted
    {                                                              //for later review
      new_state = last_state;
    }
         
    if(ADC12MEM0>= 0X9BB)                 // If voltage is larger than this number, light LED
      P6OUT |= 0x02;                                 // P6.1 = 1
    
    else
      P6OUT &= ~0x02;                       // NAND P6 Port with 0x02, should turn
                                                             //off LED ON P6.1
   
    __bic_SR_register_on_exit(LPM0_bits);   // Exit active CPU
    default: break;
  }
}