Alternator whine is usually caused by a ground loop or insufficient noise filtering on the power leads to the equipment.
Make sure all your components (empeg, amps, etc) are all grounded to the same point on the car with heavy-gauge wire. Then make sure that you've got a noise filter on the power lead to the Empeg.
In my car, I have a heavy-duty 20-amp noise filter on the main power lead that drives both the Empeg and the amps. You may not need to go to that extreme length, but I have three amplifiers, all with different ground potentials, so I'm having some ground loop troubles. A ground loop isolator may also help.
For more information on noise reduction in the car, refer to the PDF files at
http://www.installdr.com/TechDocs.html (scroll down to the "reducing and eliminating engine whines..." section).
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Tony Fabris