No, you CANNOT connect an iPod to the BOOM!’s 3.5mm AUX Jack and have music come out the Bose SoundDock . The 3.5mm AUX Jack of the CoolStream BOOM! only supports audio out. Music (or any audio) can only go in to the CoolStream BOOM! through Bluetooth. Music can come out either through the 30 Pin Connector or through the 3.5mm AUX Jack.
You can use the BOOM!’s 3.5mm AUX Jack to connect it to a speaker that has an Aux-in port or to a pair of wired headphones. By connecting the BOOM! to these devices they now become a Bluetooth speaker or Bluetooth headphones.

For more information on using the BOOM! on battery click here