My aftermarket head unit is powered through the stock harness and I haven't had any issues, but the box is also grounded to the chassis with an external ground (in other words, there is a ground wire coming from the HU to a bolt in the mounting frame). Many headunits ground the box through the mounting bolts, so you should make sure that is a good metal on metal connection if that applies to you.
Also double check the ground on your amp. The seat brackets are painted and don't fit exactly flush. Make sure your ground is making a good metal-on-metal contact - use sandpaper to make sure both surfaces are clean and bare.
Also consider where your speaker wires are running - that wire is usually unshielded and susceptable to interference, particularly from the power lines.
If I checked both the grounds to my HU and the ground to my amp and was still having big interference problems, I would probably pull out the seats and carpet and fire up the radio with most of the wires exposed - that way you could move them around to see if the whine goes away. I normally like to do this before I put my interior back together just because it's a lot of work if you have to pull everything back out again.
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