Head-units do not actually power an amp, we just use the convenience of the amps remote turn-on to wake the amp up. If your Ipod is connected directly to the amp as your signal source, you do not need the head-unit, although there are some advantages to running the weak head-phone signal from the ipod through the head-unit to the amp.
If you head-unit flip-down face to load a CD, look for a reset button behind the face. If not, power it down by unplugging the power cable.
If you want to do away completely with the head-unit, it can be done.
Michael
Mikes Liquid Audio