The pins are used to set the high score thresholds for earning free games (assuming you have it set for "credit" and not "extra ball"). You can get score cards for your game here if you don't have them: http://www.pinballrebel.com/pinball/cards/

See page 5 of your manual - there may also be a card in your backbox that shows the settings. So, for example to set 520,000, you plug one of the pins connected to the white wire (used for 510,000 to 600,000 range) into the 20,000 location. And to set 780,000 for example, plug a pin on the orange wire (used for the 710,000 to 800,000) into the 80,000 location. The other pins on wires can be simply stored in the holes in the wood.

IMG_1611 (resized).JPGScreen Shot 2019-10-06 at 6.57.59 PM (resized).png
Screen Shot 2019-10-06 at 7.19.33 PM (resized).png