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thats a myth, about running them down the same side.
anyway, first you need equal ground and power. So upgrade your ground to 4 gauge if your power wire is 4 gauge.
Electricity flows from negative to positive.
Second, how do you KNOW you are getting a good ground? did you check it with a multi meter?
drill into the chassis and use a wire brush to get down to bare metal.
If you are still getting alternator whine its probably coming through on a ground loop.
run a 10 gauge wire from your amp's ground to your head units ground. If the problem goes away then you probably need to upgrade your head unit's ground. take some 10 or 12 gauge and ground it to the frame. the factory dash grounds tend to suck ass.
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