You will normally leave the jumpers on the CPU card at their default settings. If you need to use certain peripherals, you will need to change some of those jumpers.
This also prevents using the external DAC as an audio interface, and means you can't initialize the on-board QVGA display.
If you change this you'll want an updated boot loader putting the console on UART-C not UART-A.
This also prevents using the external DAC as an audio interface.
To use the camera interface you'll need a custom card (on the PCI-format connector) connect a video sensor.
All the signals for the second SPI controller are available on GPIO lines and accessed through the J1 jumper block. Say "y" here to configure that SPI controller.
Select this if you have jumpered the J2 jumper block to the LED0..LED7 amber leds, or to the RGB leds, using a ten-pin IDC cable. A default "heartbeat" trigger is provided, but you can of course override this.
Select this if J2 is jumpered to LED0..LED7 amber leds.
Select this if J2 is jumpered to the RGB leds.