Engine noise. Please help

Ok, here's the scoop.  My system was completely fine until I started to upgrade.  I've always had subs in my car.  They work fine.  Never had ANY problems with them, at least with engine noise.  Recently, I have been upgrading my system.  I have put brand new Pioneer 4x6's in.  Model # TS-A4670R.  They are 3-way speakers.  The RMS on these speakers are 2-20 watts with a max of 120 watts per speaker.  These are my front door speakers.  I purchased Pioneer 6x9's for my back speakers.  Model # TS-A6990R.  These speakers are 400 watts max and 80 watts RMS.  They are 4 ohm speakers.  An Alpine MRV-T320 2-channel Amplifier running my 6x9's.  This amplifier is 400 watts max bridged at 14.4V (when the car is running), 140 watts max  x 2 at 14.4V.  ok, too many specs to list.  You get the idea.  I have tried everything to get the whine out of my Alpine amp.  I have taken my car to Auto One and they said that my amp is bad.  It's impossible.  It's brand new.  I had a Rockford amp that was a refurb and it still had the whine.  So, that is why I bought the Alpine because I thought it was the amp.  The Alpine amp is grounded in my truck, underneath my carpet, stripped of paint.  My car is a 1999 Grand Am SE.  I've seperated my ground from my subwoofer amplifier (Rockford 801s) because they were running to the same point.  I've made sure the power wires are running down the left side of my car and RCA's down the right.  The memory is on the left with the power.  I've bought 3 sets of RCA's so it can't be them (had cheap ones, bought Rockford Fosgate and didn't work, then bought Monster Cable and didn't work).  I have a Pioneer DEH-P9600MP head unit.  The RCA's to this amp are hooked up into the back of my head unit to the RCA inputs that say "Rear Out".  I only hear the engine whinning when the car is started.  If the car is off and the key is turned, I don't hear any engine whinning.  Do you think that the head unit isn't grounded properly?  If so, then wouldn't the front speakers do it too?  I unplugged the RCA's to my 6x9's a while back because the engine whinning was so unbearable.  All I was using was my front 4x6's and my subs and there was no whinning.  My 4x6's by the way are running off of my head unit.  I have not cut off the wires running from my head unit to my back speakers, you know, the white and grey wires running out of the head unit.  Do you think that those wires laying on top of the back of my car where they could be touching metal could be doing this?  Unlikely but work asking.  Please help me.Will Irizarry

I did have both amps grounded to the same ground.  The ground is a little bigger gauge then the power.  Also, something I forgot to add, when I step on the gas, it gets louder.  But the weirdiest thing is, that I have power windows.  Recently, my passenger front window motor broke down.  I bought a new one and installed it.  When the engine whinning started, I noticed that when I roll down that window, more whinning comes through the rear speakers.  It doesn't do it with any of the other windows.  When I step on the brake, I hear a little pop when the brake is applied and a little pop when I let off of the brake.  Now, my stock 6x9's that came with the car has a really weird hook up.  Most speakers have a positive and a negetive.  It seemed like these stock speakers had dual voice coils because it had to sets of positive and negetive inputs on the speaker.  It was hard to get these off the way they had them so I had to cut one of them off, meaning 2 wires that come from the head unit to the back left speaker are exposed and not closed off.  It is close to bear metal.  I was thinking this could be a problem.  Am I right?  Should I try splicing into the ground in the back of my head unit to go to my amp?  I've tried almost everything.  Now, I do have my rca's and power wires seperated, but I will admit, they are kinda clustered in the back where they go into.  The guys at Auto One took a wire and touched it on the ground on the amp and on the ground RCA coming into the amp and it cut down the noise but not totally.  That's why they said that the amp is bad.  There is no way that I can get 2 amps in a row that are bad.  Give me any suggestion.  There has got to be something wrong.Will Irizarry