Solar Powered Arduino Due

I am designing a solar powered Arduino Due for an intelligent small organic farm irrigation control. I am using AdaFruit solar panel and their Li battery charger (http://www.adafruit.com/products/390), plus the AdaFruit boost converter (http://www.adafruit.com/products/2030). This lineup gets me 5.2VDC from a solar/Li battery configuration.

My question is how to connect it to the Due in as native a way as possible.

Vin needs to be between 7-12VDC so I can't use that. I really like AdaFruit and all their boost converters only go to 5VDC hence a bit of a constraint.

My plan was to connect the output of the Boost Converter (USB) directly to the Native USB Programming Port of the Arduino. This would make the native USB port my input power source and I would not use it for communication. I would then use the USB programming port concurrently for programming activities. In the deployed solution it would be only the sun for power and programming port left unconnected.

I understand that the Due is smart enough to select between USB and external power source, but can it contend with my PC also driving 5V on the USB programming port along with my boost converter driving 5V on the native USB port.

Things for sharing any wisdom?

I don't know the answer but wondering why you need the solar source while it has the programming USB source available to use for power?

Development will be done connected to a computer. Once I deploy the solution it will be on a 20 acre farm so all power for entire solution will come from the sun.

That will be fine so long as there are no other connections in the system. You aren't planning on having the programming laptop powered from the same solar system or earthing everything to an earth stake? The two 5V power supplies will sort it out between themselves - you're really connecting two independent battery-operated systems together.

Thanks MorganS. As I think through this a bit more I realized that for development with my Computer at home, I will power the Arduino through the programming USB port as I won't be using solar power. The native usb port will be disconnected in this case. Whenever I use the system for its application, I will not be connecting to the USB programming port but instead only the Native USB port to get power from the Boost converter connected to the battery charger.