Flashing Due with latest IDE (1.8.5)

Hi all,
I am migrating to Atmel Studio 7 and need to configure an external tool to program my new Due board.
On other forum i read that Due is programmed using Bossac, but this program is not in the latest Arduino IDE.
It appears that there is no up to date info about this topic, then.
How is Due programmed these days?
I have also read that it is possible to program a Due board using the other port ("native"); is it true? how is it done?.
Final question: is it possible to program a Due without having to press the Erase button in the middle of the card? When i put a shield on it it is impossible to reach it.
Thanks and regards

You need to install Due support in recent versions of the Arduino IDE:
Tools > Board > Boards Manager > Arduino SAM Boards > Install

That will install the Bossac tool.