When the AREF0/AREF1 jumper is disconnected, the ADC reference voltage can be supplied from an external source by connecting to the AREF0/AREF pins on the AUX header.
When using an external source for AREF, VTARGET must be controlled at a higher voltage level than AREF. This can easily be controlled by reading the VTG value from the programming dialog in Atmel Studio before setting AREF.
Note: The AREF0 and AREF1 voltages, which are
visible in the PC software, are the STK600 generated voltages. Externally applied AREF
voltages cannot be read from Atmel Studio.