I had 2 12s in my 89 z28 with 2600watts going to them and didn't have the whine added a distribution block to add a mids amp and I get a whine coming from the 6x9s hooked up to it the 12s and door speakers are fine its just the 2 hooked up to the new amp what can be done to fix this ther both grounded right next to each other (separate grounds) and I don't get the whine when I just run the ignition on acc

 

Sounds like you might need a noise filter either on the speakers or the amp.

 

wouldn't tht be considered just a patch/Band-Aid not really fixing the problem

 

I had a similar problem, but it started when I went to dual alternators. I was getting a serious RPM whine, tried noise filters on the deck, amp and even a alt supressor, no fix. Then I tried a ground loop noise supressor (RCA type) by Stinger, no fix. Swapped out my deck with another Pioneer deck and... no fix. Finally out of curiosity I tried my friends Kenwood deck and the noise was gone so I bought a Kenwood and alls good.
Disconnect your RCA from that amp and see if the noise is there, if so, then its possibly gound loop. If it goes away then its signal sent. Next reconnect RCAs to the amp and disconnect RCA from deck, if its still there, possible power wire interfearence or bad RCA, if its gone then still signal sent from deck. Now some decks have stronger built in noise supressors than others and a filter may be the only fix. Check the plug wires on the engine for splits or burns as this can cause RF signals to get their way into the stereo systems components.
I hope this helps