What you need to do it wire the remote turn on wires to trigger the factory amp to turn on. In the bmw harness you will see a white wire. THis white wire needs to see positive 12 volts when the radio is on and 0 or negative when the radio is off.
The remote turn on wires from the pioneer deck is blue with white stripe.
The remote turn on wires from the factory amp is white.
This will solve your problem.