HU straight into aftermarket amp?

One question is what you are you trying to acheive overall?
If you are an audiophile type and most interested in getting the purest signal possible then doing something like bypassing the JBL amp might be something to look at.
But if you are just interested in pumping up the volume maybe you just need to tap into the rear speaker high level outputs, pass the signal through a high-to-low level converter, and add a subwoofer and amp. Also, replacing the door speakers with more efficient ones should help. This is what I have done. System rocks and I still have full control of volume through the OEM controls.
Someone else may be able to answer your questions if you're more interested in the former. Good luck! B)

 

I think bypassing the JBL amp only makes sense if you are going to add an equalizer and volume control. I'm considering doing just that. The biggest issue I've found so far is that when changing sources e.g. from Radio to CD, I get a popping sound that I think the JBL amp muted. I'm still looking into finding and easy way to mute that (there is a mute signal in the wiring to the JBL amp).

The dilemna is that most muting circuits I've found are not really high quality, and I hate to degrade the signal with a poor muting circuit; might as well just go through the JBL.

Also note that the EQ that the JBL does is generally good and useful above the bass region, and I think the loudness functionality is actually useful. I may end up just leaving the JBL amp in the circuit for the loudness.

 

The peaks and dips in the JBL amp response above the bass region seem to be there for good reason, to do "room correction" and probably some psychoacoustic stuff. I probably need to update my document on this count; I used to think they were more evil than I do now. For a few months now my system has been just the JBL amp rear channel driving new Focal speakers up front. It sounds quite good, I think mostly because of the work I did on b-quieting the doors and using good Focal drivers.

You can certainly plug an ipod directly into aftermarket amps if you want to avoid the Prius electronics completely. Another option is the new JL Audio switcher.

Another reason I wanted to tap into the pre-JBL signal was so I could switch between external sat receivers, mp3 players, and the factory HU, all with flat EQ. That way I won't have to change the aftermarket EQ preset when I change sources.