a) you need a common ground - in other words, you should power your arduino and your boss effect with the same power source and connect the grounds as well.
b) check the voltage between the LED and ground with a multimeter. You don't want it to exceed 5v. If it does, use a voltage divider to divert enough voltage away from the Arduinos input.
btw. this thread should probably be in the "device hacking" or "general electronics" sub-forum. You would get a lot more feedback there. Maybe ask a moderator to move it.
regards
p.