Originally Posted by kaigoss69
Whenever possible, DO NOT use the headphone out of the iPod. It has to do with a mismatch in out- and input impedances and voltages. The headphone output is optimized for driving HEADPHONES only. The line output is optimized for aux inputs and it bypasses the iPod's volume and EQ settings to give a flat, strong signal.
I don't believe it will bypass eq, based on experience. I do however recommend use of the dock connector.