The dedicated SPI is just SPI, I think, there is only one SPI supported by the Due SPI library. The Due pins are numbered D74,D75 and D76 and these are the pins used by SPI lib.
I'm not sure about the SPI-CSx pins, are they used in Master or Slave mode? SPI-CS3 is not mapped anywhere (unconnected on SAM3X), so if you don't want SS/CS then specifying BOARD_SPI_SS3 will ensure the SPI does not interfere with other pins.