I have been looking at the datasheet and was equally confused. Looking at the datasheet for the ADC on a similar Atmel microcontroller (SAM3S) suggests the following:
In free-run mode the TRACKTIM and TRANSFER fields of the Mode Register are used to set the tracking and transfer timings. The tracking time needs to be set depending on the source impedance, but I still don't understand what determines the transfer time.
In triggered mode set TRACKTIM=0 and TRANSFER=1. Depending on the source impedance the details in the electrical characteristics section allow a tracking time to be calculated and this can then be used to calculate the sampling frequency. The sampling frequency should be between 0.05 and 1 MHz.
Can anyone who really knows confirm this and explain how to determine the transfer time?