Just wanted to make sure on this one. Is the LED pad on the Green Bean for the anode? Or does it matter? I'm using a 3pdt board with a single LED pad. So I'm assuming I should run the anode to the green bean and the cathode to the 3pdt board. Is this correct?
Yep. Check out top right of the Green Bean schematic. It doesn't show the LED itself, but you can see that the pad runs to the +9V through the current-limiting resistor. Then check out the Standard Wiring Diagram (http://www.madbeanpedals.com/tutorials/downloads/StandardWiring_MBP.pdf). The anode (rounded side) connects to the positive voltage and the cathode (flat side) connects to the switch. Activating the effect at the footswitch will ground the cathode and allow current to flow through the LED.