I have a problem with Ignition noise (I think?)
Is it a whine, or a regular clicking noise? If it's whine, then it's probably caused directly or indirectly by spurious AC coming from the alternator. If it's a clicking, then it's more likely to be either ignition or injector noise.
Further to what Hugo's said, try running the Empeg power ground lead to the same earth point in the vehicle as the amp, make sure that the filter in the feed to the Empeg isn't anywhere near the signal cables at the back of the unit, and that your signal cables are run well away from any original cabling in the car.
If you've tried all of that, and you're still having problems, feel free to email me directly (avantg@btinternet.com), and I'll see what else I can come up with.
Dominic
Cambridge Car Audio
http://www.cambscaraudio.co.uk