I usually work with pics but see if this applies:
There are 2 byte registers containing the 10 bit reading called ADRESH and ADRESL, they can set to either left or right justify.
All I do is to:
Int reading = 0;
//do adc conversion
reading = ADRESL;
reading += (ADRESH*256);
Something like this, so the register that contains the appropriate 9th and 10th bit gets multiplied by 256. The total value is stored in the int variable reading.