Replacing HU

The easiest way to go may be simply to use the factory wiring as much as possible, which already passes through the nav unit on the way to the front left woofer. So just have the installer run speaker wires down from the new head unit to the factory wiring which is accessible where it enters the JBL amp under the passenger seat. You can even buy the bazooka harness so you can tap in without cutting the factory wires.

Then in the doors you wire your aftermarket speakers to the factory speaker wires.

 

Basically, Yes. The NAV system expects an amplified signal. When it wants to use the speaker it simply disconnects the normal feed and sends out it's own amplified signal.

I set up my system this way. Line level RCA's from the new deck to the new amp and then from the new amp to the speakers using the existing wiring. This made everything easier as all the wires already ran to the location of the new amp (under the passenger seat). I would have rather used new wiring (with a lower gauge wire) but I did not want to go through the hassle of feeding wire into the doors (the prius does not have any convenient holes to slip the wire through, just a solid plug with all the wires for the door).

Also if you plan to remove the old head unit you will need to terminate the bus wires that run from the old head unit to the MFD. I used a 47Ohm resister and it worked fine.

 

Almost forgot,

I don't know how the mute signal from the NAV system can be interfaced with a new head unit, so Bluetooth and NAV will still work fine but the stereo will not auto mute when you receive a call.