i read SAM3X comes out from ATMEL with ROM flashed yet.
Yes the SAM has UART and USB bootloaders hardwired in ROM.
what about the ATMEGA16U2? i need to flash it, right?
Correct. You would provide a method to program via the SPI port.
If it's a one-off programming job (ie just the bootloader) then put 6 pads somewhere on the board that allow the connection of an ISP cable somehow. Some methods I know of are...
If you have the space add a standard 2x3 header footprint but offset the middle two holes a little bit so the header is an interference fit and will stay there by itself while programming.
Another way is to have two rows of pads on the edge of the board, 3 pads on each side. This allows you to slide a header onto the board for programming (you will have to bend the header pins a little to get a firm fit).
And another way is to have a very small footprint of 6 pads and use "pogo pins" to make the connection for programming.
There is also a special connector designed to clip into a matching footprint on the board, unfortunately I can't find the details right now.
And finally you can program the chip in a ZIF socket before soldering it in, this might be OK for a mass-produce item but it means you can never change the program so not a great idea normally I think.