Ground loops are caused by multiple return paths with different voltage potentials between them. Alternator whine is a function of the electronics ability to isolate from noise on the supply rail. That being said, I have a basic rule I follow when doing car installs (and I have done more than I care to remember). Bring +12v and ground from the battery posts using a suitable gauge wire to support your total system load (amps, x-overs, headunit, etc.) to the area you will be mounting your amplifiers (by far the highest consumers of current). Then, using distribution blocks, run power and ground leads from there for all equipment. No exceptions. If you're really worried, then isolate the accesory input to your headunit with a small relay, so your headunit is only supplied from the block (not typically nescessary). This way your car battery acts as a big alternator noise suppressor (it's low impedance) and ground loops... well, what ground loops ?
Works every time