Burn bootloader and program SAM3X

Hi, I'm in the final stages of a project based on SAM3X and so I'm building a [u]very[/u] barebones Due with only the pins I need. But while that's still in progress I'm wondering about a couple things

1) On a fresh SAM3X before I can [u]program it with Arduino IDE (a requirement for my project)[/u], I understand that I need to burn the bootloader. What are my options for going about this? Do I have to build a Atmega16u2 breakout board or build that into my design? And if I have to do either, will I have to burn a bootloader for the Atmega16u2 or program it? This part's a bit over my head.

2) I've noticed on my Due I can use the Native USB port or the Programming port to program the SAM3X. What's the point of the programming port then?

anyone here knowledgeable about this?

There is no bootloader to burn. The chip works straight out of the box.

The native USB uses the main processor. If you have uploaded a misbehaving sketch and it has locked up then the native USB stops working. Usually I just press the erase button and native works again.