Arduino Due and Vin, 3.3V and 5V power inputs
DC Jack is connected, through a diode, to Vin.

Vin is stepped down to 5V on-board.

5V is stepped down to 3V3 on board.

Thus you can do any one of the following numbered items.


Connect a 7-12V supply to the DC Jack; thus:


use Vin as a supply @ DC - 0.7V for off-board peripherals, and
use 5V as a supply for off-board peripherals, and
use 3V3 as a supply for off-board peripherals.

Connect a 6-12V supply to Vin; thus:


use 5V as a supply for off-board peripherals, and
use 3V3 as a supply for off-board peripherals.

Connect 5V supply to the 5V; thus:


use 3V3 as a supply for off-board peripherals.



The above is only guaranteed for boards that follow the reference schematic, as plenty of clone/compatible boards do. If you buy a cheap Chinarduino and something doesn't work, or the thing breaks, after following anything above then that's your tough luck.