Disconnect the RCA cables going to the new amp, if it still produces whine then the noise is coming in on the Power. Likely a bad ground loop as Glen pointed out. There should only be one ground for the system. If the noise goes away then the noise is likely coming in on the RCA cables. Reroute them away from ALL power sources or even try a different set.
Might even be the amp it self. Is it mounted on wood or screwed to the sheetmetal? If it is directly attached to metal then you have TWO grounds. Try mounting it on a piece of plywood to isolate the case from the car chassis.

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'91 Laser RS Turbo-"Sound Advice" guy.
www.geocities.com/motorcity/speedway/5051
Turbo + Intercooler = The replacement for Displacement

'06 Magnum R/T (Yeah -it's got a HEMI!) Mods beginning!