is your amp and headunit grounded to the same spot on the car to eliminate grounding loops?

No, they aren't. I have two separate amps, and one of them is in the trunk, making a common ground difficult. The front amp is ground to the same point as the head unit (the in-dash radio wiring harness). The noise filter is on the power lead that goes to the front amp and the head unit, and is grounded to the chassis (as per its instructions). The amp in the trunk is getting its power directly from the battery and is grounded to the chassis in the trunk.

I've had four different head units (counting the Empeg) with the same amplification setup. Ground loops have never been a big problem for the most part. One of the head units I had would make some electronic noise similar to the Empeg, but others have not.

I'm not totally clear on the concept of a ground loop, and I'd love to hear more about it if you're an expert on the subject.