J301
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.
J500
This jumper is used to enable the 512k of (SLOW) 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.