These setting come out of the manual for an Amiga 2000 Revision 4.x and is compliant with REV6.x Amiga 2000 boards as well.
This jumper determines the high order address bit for Fat Agnus.In it's normal position, the high-order bit is A23; in it's other position, this bit is A19. The current Fat Agnus chip requires the A23 signal for proper management of the memory at $C00000. Future Fat Agnus chips may may things differently; this keeps the current board compatible with simple enhancements.
This jumper determines the time base used for the 50/60Hz CIA timer chip. In the normal posistion, the 50/60 TICK clock, based on AC line frequency, is used as a time base. In the alternate position, the verticle sync pulse from the video section is used. The system will not operate properly without one of these clocks.
This jumper is closed to add a second internal floppy drive, open to leave the second floppy out of the main unit box. The Amiga expects an ID bit stream from each floppy drive; this lets it determine the drive type. External floppies have this ID circuitry on board, but as it's not an industry standard capability, it has to be implemented on the A2000 motherboard to save cost on internal drives. Leaving the jumper open prevents the Amiga from seeing the ID sequence.
This jumper is used to enable the 512k of RAM at $C00000 and the real-time clock. It is normally closed; opening it will disable both this extra RAM and the real-time clock.