Okay then if you are only using the EQ alone then set the dual zone levels on the EQ control panel at full before gaining the amplifier. The ipod shouldn't have enough voltage to drive the EQ into clipping which you can verify in the same manner you would with a HU. Some will set the EQ levels at 90 percent to allow for a little extra gain when using material that is recorded a bit soft or when using another mp3 with less gain. Building in some small amount of flexibility isn't going to hurt your tuning objectives.

David
Earmark Marine