Sendero,
I suggest you do a search on users ellweber and clownburner in both the technical and installation forums. All three of us have done installs in our Boxsters with similar initial alternator whine and ground curent noises from the Empeg (easiest to hear when the engine is off).

You can get whine and other ground loop noise down to very low levels with aggressive (I mean AGGRESSIVE) grounding between the Becker and Empeg chassis. This means one or more heavy gauge wire or braided straps bolted to the Empeg sled and either bolted or pressure fitted at the Becker frame. BTW, it's a lot easier to work on and reinstall the Becker if you remove the A/C panel (or cupholder) above it. An additional high quality power line filter to the Empeg can help a little more with Empeg DC current noises. I ended up using a DC-DC inverter to power the Empeg and it's dead silent (but probably overkill for all practical purposes).

In both approaches, you'll still need to be very careful about routing the RCA cables (ellweber used only a male-to-male adapter to minimize signal path) between the two units since there are a number of noise sources in the console that can easily inductively couple to the audio cables.

BTW, you can also use ground loop isolators (Crutchfield, Radio Shack et al) to connect the audio. With these, you can pretty much ignore grounding issues. But these transformer coupled devices degrade the audio quality; especially at the low end (my bench tests confirmed this on the Radio Shack coupler) and still require careful routing to avoid inductive pickup that will cause alternator whine and general switching current noise.

Hope this helps. Good luck!