OK, that's what I thought. When powered up, my controllers just sit and wait for an audio input so there's two ways to go about controlling the audio. If you have a way to create multiple channel audio files (Audacity can) it's just a matter of connecting the proper channel to each prop. Now, you can control two skulls from just one stereo audio feed by removing the appropriate jumper from my boards, each one will only respond to the specified channel.
The other option is to have separate triggerable mp3 players, but that requires an additional controller which is programmed to trigger them at the proper time. Since you also wanna control lights, this would probably be the best way to go. A lot of people like Arduinos for this, I personally don't use them as I make my own controllers with various PIC's. Microcontrollers like these do require writing program code to load onto the controller, it's not too difficult but there is a learning curve.