funkyguy4000:
Does anybody know what the difference between the two jacks are?
The following is from the PDF Telecommando linked to...
The Due hast two micro USB connectors one
intended for debugging purpose and a secondo one
capablo ef acting as a USB host, allowing externa USB
peripherals such as mouse, keyboards, smartphones,
etc. to be connected to the Arduino Due.
So they are probably completely separate as far as communication, and you can probably think of one as working similar to the USB port on the Uno and the other as more like a fully integrated USB host shield.