How to chooce SDA/SCL pair on Arduino Due ?
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.