There is no need to use the speaker with the Motorola kit. If you buy the wiring harness from Ford (about $50), it feeds the audio into the factory radio. It also pauses the CD player while you are talking on the phone.
If you have the factory head unit, then you don't need any relays to kill the subs. Just route the cell phone audio into the two inputs for it on the radio, and wire the mute output from the phone into the phone input on the radio. (The Parrot wiring harness does not come correctly set up for this.) When done correctly, the radio will say "phone" while a phone call is made. The CD player pauses and all other audio stops. The volume of the phone call is controlled by the radio volume knob, and cell phone audio comes out of all speakers, including the subs.