Nanduino » Power Options
The Nanduino mirrors the flexible power options offered by the AT90USB162 microcontroller. You can power the board from the host's USB port, which is fine for low-power (<500mA) devices. Or you can supply an external 5V supply. The board can be directly powered by either of these 5V sources, or you can choose to use the output of a 3.3V regulator built into the micro. The latter is useful when interfacing with components which are not 5V-tolerant, a good example being SD-cards.
Power Source
The left-hand column of three jumpers on the board is for selecting the power source. Connecting a jumper between the bottom two pins will select USB-power:

Alternatively you can connect a 5V supply to the top two pins, with the polarity thus:

5V or 3.3V?
The right-hand column of three jumpers on the board is for selecting between a 5V supply and a 3.3V supply regulated by the micro's internal regulator. To use the 5V supply directly, put a jumper between the bottom two pins, thus:

Alternatively, to use the output of the micro's internal 3.3V regulator to power the board, put a jumper between the top two pins, thus:

Note that there is only enough power from the regulator to supply about 50mA at 3.3V.
Other Power Options
It is possible to run the board with an external 3.3V supply, if the internal 50mA supply is insufficient. In this case the external supply should be connected similarly to the external 5V supply, but this time you should connect all three of the right-hand column of pins together, and disable the internal regulator by doing REGDIS |= 0x01 soon after RESET. Failure to do so will significantly lower the life-expectancy of the micro.