You do not need to supply the -VREF with a dual-rail supply.
"Note that neither a negative supply, nor a supply larger than VDD (unregulated power)can be applied to these pins. It is the difference between the pairs that are converted in differential mode."
My first question would be what is the voltage range of your sine wave? If your VDD is at 3v, then neither pin6 nor pin7 may exceed 3v or 0v.
The ADC outputs a 2's compliment value. Here's my formula for converting 2's compliment to negative numbers on a PC:
Let's say
ADCResult = ADCH * 256 + ADCL; ///This would depend on how you're sending / receiving the data...
if ADCResult > 2047
{
ADCResultSigned= ADCResult - 4096;
}