Yes for (1) and (2)
The answer for (3) is: no, you can't with SAM-BA bootloader.
Using SAM-BA bootloader you can upload a file in two way:
- from UART (pins RX0/TX0 on the Due Board at 115200bps N81).
- using USB, if you connect the board to a PC the board is seen as a virtual serial port. SAMBA has a little USB Device driver for serial port emulation.
So, forget mass storage devices, unless you write your own bootloader that handles USB Host OTG, but this is another story...