Are you using RCA ground loop isolator or one that attaches to the power wire of your amp/hu?
If its RCA's connect at either end I believe..
If its Power wires then I would say connect it to whatever device is creating the whine.. I did this in my moms car by connecting a speaker to the speaker wires on the hu and listening for the whine.. since there was none I know the whine was being created by the amp or RCA's and not the HU, so I got a ground loop isolator for use on RCA's and connected one at each amp. Problem solved. Since then I moved the RCA's to the opposite end of the car and removed the ground loop isolators, you can only hear the whine now if the HU is on and the volume is all the way down.. but even then its minimal.
Good luck! //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif