I'm planning to power the board up via external power supply. After looking at its schematic diagram, I found that one can supply power through 5V pin or 3V pin on the headers. But I wonder if you could have problem, when you would connect this board to 5V external power supply and PC also.
You can download the schematic diagram here http://www.st.com/en/evaluation-tools/32f429idiscovery.html
From my understanding it is just fine, since you are having two 5V power supplies. But I'm not confident and afraid of breaking my board. It would be appreciated when you would give me answer.