One USB port is connected directly to the processor and has an OTG connector, this means that it can be used as an USB host to connect devices like mouse, keyboard, android phones etc
The Second USB port is connected to the UART0 via the usual atmega16u2 we use on the other boards. this port is used for programming and communicating with the board. This allows you to develop projects using the USB host without having to plug and unplug cables all the time.
The board has a 4 pin SWD connector that can be used to debug code using a SWD/JTAG dongle. There is also a footprint for a 14pin jtag connector.
The pictures robotgrrl posted on the flickr account are of an old beta board we gave out in may to a number of beta testers and it didn't have the second USB port.
We upgraded the power supply to a DCDC converter that can provide enough current to the USB host so that now the Due can be used as an ADK2 development board
if you have other questions, shoot!
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