Tom hit the nail right on the head. the problem is a poor install. you need to re-do the system to get rid of the alternator whine. here are some things to keep in mind:
1. run power lines on one side of the car, and signal lines on the other. also, get quality cables. spending a little extra can save you a lot of headaches in the future.
2. if power and signal lines must cross, make sure they cross at 90 degrees. i used zip ties to keep them perpendicular.
3. make u'r ground wires for the amps as short as possible and use different ground points for each amp. if you have multiple amps sharing a ground point, make sure the amp with the most power output is the first one touching the ground.
following the above advice should help with your alternator whine.
-j