Setting up the XMEGA ADC can be a bit confusing. There are two basic set-ups I use:
1. Single ended, GND to AREF with zero at GND, 0-2048 (11 bits). Set signed mode (CONVMODE bit) and single ended mode (SINGLEENDED bits).
2. Differential, GND to AREF with zero at MUXNEG, -2048 to +2048 (12 bits). Set signed mode (CONVMODE bit) and differential mode (DIFF bits).