I was able to figure it out.
I connected the Arduino directly to the controls. When the Arduino control isn't being used, I have pinMode(INPUT), this allows for manual and remote (Finger button press and IR remote) control. When controlling it programmatically, I use pinMode(OUTPUT),digitalWrite(pin,LOW).
Now I'm figuring out how to sense a LED. Not connecting a phototransistor type device to it, no room. The voltage difference is 60mV when the LED is high, but analogRead isn't picking it up, might have a different GND then currently plugged into.