2006 Grand Cherokee Speaker Wiring

I have a 06 Grand Cherokee with the 6 cd changer with Nav and sat radio with 6 speakers I'm replacing the head unit with a new one and adding an amp with one 10" subwoofer. I'm planning on keeping the dash tweeters and replacing all 4 door speakers. The head unit will drive the 6 stock speakers and the separate amp will power the subwoofer. My issue is the connectors have been cut-off so all I have is wires I know where the power ones and ground go but the speakers have 2 wire pairs and a couple of 3 wires strands but I can't find anything that shows how the 3 wire strands attach to the speakers and the twisted pairs their colors don't match up with anything, so I'm needing some help here because no diagrams show me the right colors for the 06. Thanks, guys for the help.Semper Fi

Is there an amplifier behind the trim in the passenger side in the cargo area?

I don't see where one would be, is that where the twisted 3 wires would go?Semper Fi

I found that in fact there is an amp in the driver's side rear trim shelf that goes to the wires I see in the dash it looks like.Semper Fi

You are going to have to bypass the amplifier. The amplifier has a digital turn on circuit. If the plug was still there you could use a 100 dollar harness to use the factory amplifier. Plug cut off = you will have to bypass the amplifier. http://metraonline.com/part/70-6504

I took the amp out already so I'll have the new head unit for the dash and door speakers and the separate amp for the one sub-woofer. I was hoping to not have to run new speaker wires but I've got pairs of wires for speakers and some 3 wires twisted together but the colors in the diagrams and mine aren't matching up. I have the main power plug and that's no big deal, but there's another speaker plug a 10 pin I believe that is for speakers but the wires again aren't matching up with what the diagrams say.Semper Fi

factory amp crosses over all speakers in the car, replacing just the door speakers will only get you mid bass and no highs. The factory stereo had a continuous left and right audio signal output along with some can wires that told the amp to turn up/down fade/balance and so on and so on. BYPASS!! just to make life easier... http://www.metraonline.com/part/70-6504 33 years as a installer now just a retired old guy. Favorite thing to install/topic are remote starts/car alarms. Stop using test lights!!!

I'm replacing everything except the dash tweeters and hopefully the speaker wires so all the old stuff (amp and head unit and all 4 door speakers) will be gone. I have 2 3-way speakers for the front doors and 2 2-way speakers for the backdoors. Then the new amp for the 10" sub-woofer. So yes, I'm bypassing and removing the old.Semper Fi