On Arduino Due, there is two pairs of pins SDA/SCL that I can use for I2C. There is SDA0 and SCL0 at, respectively, pins 20 and 21 and an another near AREF. How do I choose which one of them I use ? I also read that 20 and 21 has built-in pull-up resistor, is that true ?
Pins 20 and 21 are the default I2C pins. A lot of libraries assume you use these, and would require some extra work to get working with SDA1/SCL1.
They also have their pullup resistors already present on the board of the Due (see schematic).
So just use pins 20 and 21, unless you have a good reason to use the other.