My Experience Installing a 5 Channel amp on a JBL Nav System

I'm posting here to help anyone that might be trying to do what I've done, so you can learn from my mistakes.
1st: I'm not a car audio pro. At. All.
What I was attempting to do:
I wanted to keep the stock speakers and use them in a separate configuration to have 2 channels of the amp for Tweeters, 2 Channels for Mid/Mid base and the other two for a sub that will be added to the back.
I figured that I would use the built in cross over function of the XD-700/5 JL amp I bought to set the speakers to their appropriate freq.
I used the High power output of the factory amp, spliced the wires directly to RCA's (as per the amp instruction manual, no need for high to low converters) and sent that to the lower power input on the new amp.
I also attempted to use the low power wires coming into the stock amp to find that I had NO volume control when I did that, so I had to resplice them back into the harness (NOT FUN!)
I wired each side of separates in parallel to achieve a total of 4ohm load on each channel. (I dont care about fade front/back) This was in fact the case on all channels except the Right side tweeters. They read 16ohm!
Because I have the factory wiring diagram I was able to see that the front right dash tweeter is also plugged into the instrument panel for seat belt beeps etc.
This poses a problem it turns out because in order to "hear" those tweeters I had to set the gain on the new amp so high that there was a unacceptable hiss throughout the volume range of the system. (Horrible!!)
Here's what I did to fix it:
Leave the factory tweeters on the stock amp!! I now have the gain turned all the way down on the amp and it sounds AMAZING! even with the stock speakers.
I couldn't be happier!!

Does anyone have a suggestion what I should do with the extra pair of channels I now have on my 5 channel amp?
For some reason when I bridged the existing channels the audio was muddy and echoey.....any pro's with some ideas?

 

Actually I am using 2 Channels on the new amp. 1 for the sub, and the other for the door speakers (excluding the tweeters that are on the JBL amp) So I only have one channel idle.
Simply amplifying the stock door speakers with the JL amp improved sound quality tremendously!
So you are thinking my speaker wire was out of Phase when I bridged the door speakers? I'm almost certain I had it right. I'll try it again to be certain...thanks!

Edit:
I checked the phase, it was correct. It looks like it's something to do with the crossover on the AMP, I'm going to have to call JL's support and see if the amp supports what I'm trying to do. Although it really sounds amazing as it is, I don't think doubling the power to the door speakers is really necessary.