OK, since this forum seems dead and I want to help those who follow... The 5V external connector (J2) has 2 sets of pads associated with it. One is R177 the other is R176. If you short (bridge, jumper, etc) R177, then the external 5V connector will be able to power the board. There appears to be no conflict with the USB micro connector. If you want to supply 5V on any of the Arduino pins, you then need to short R176. Then the 5V will come out on the appropriate Arduino pins. But, beware, the SAMA5D3 Xplained is a 3.3v card. Don't put any 5V shields on the unit or you'll toast the CPU. I just needed 5V for an external circuit.