While trouble-shooting my installation, I have had the amplifier connected
temporarily in the passenger footwell, where it works very well indeed.
Now that I am ready to install the amp properly in the boot, I am faced
with a grounding dilemma.

So far, I've been using a long, chunky 12V 30A cable supplied with the
amplifier run directly from the battery (in the boot). The amplifier
is connected by a short, equally chunky ground lead to the empeg sled,
which is in turn connected to the relatively flimsy ground lead supplied
by the car for the head unit. Digital playback is excellent, with no
trace of noise, although I do get faint alternator hum on FM (which I
might perhaps become the subject of another post:-).

Now when I move the amplifier in to the boot, I can shorten the 12V
supply cable, which is good, and give it its own grounding point, which
is particularly good since I've not been too happy with using the rather
feeble-looking ground supplied in the centre console anyway. But now,
what do I do about grounding the empeg? From what I've read, it sounds
as if I should take a chunky ground lead from the amplifier to the empeg.
But do I ground at the amplifier end or the emeg end, or both?

There should be a ground wire on the empeg docking sled for that purpose.

Ground the amp in the boot with a suitable (thick) cable. Don't run it directly to the sled.
Then run a wire from the empeg to the grounding point of the amp (not to the amp itself, to the grounding point, very important). That wire does not have to be thick. 0.75mm² will do fine.
Don't ground the amp directly at the battery.
If you still have ground loops, sometimes it helps to isolate the amplifier's case from the body of the car (by mounting it on a piece of MDF or so).

Frank

Then run a wire from the empeg to the grounding point of the amp

By lengthening the groundwire coming from the empeg, you are increasing its resistance. This has the potential to induce a ground loop. I would only do this as a troubleshooting step, and only with a very heavy gauge ground wire.

Normally, you would ground the amp to the car frame in the trunk, and ground the empeg to a proper ground in the dash. In most cases, the ground wire on the car's wiring harness is plenty for this task. The only time you would need to do anything else is if you've already hooked it up this way and you're having to troubleshoot a noise problem. If I recall correctly, the initial post in this thread didn't say if he'd already tried it this way first.

FWIW, I do this every time I install an amp (been selling car hifi for 10 years now). I can't recall it ever inducing a ground loop, yet it cured * a lot * of them ...
It never hurts to install the wire while you have the car apart anyway. It's easier to disconnect the wire should it cause a problem than having to tear the car apart again to run an additional wire.

Frank

Agreed that running extra wires while you've got the car apart is a good thing.