Alright.

As of yesterday, this is my current setup:
98 Honda Civic EX Coupe
empeg in dash:
- yellow (constant) line put directly to the battery (in-line fuse used, of course).
- red (switched or ignition) line is wired to the Honda harness, sharing it with the red line from the CD receiver.
- black (ground) is wired to a part of the frame (bare metal) of the dashboard, just behind the glovebox.
- white (headlight sense) line is wired to the orange/white line (headlight sense) from the Honda harness.
- green & blue wires not used, covered by electrical tape.

CD receiver mounted behind shifter, in space originally meant for Honda CD changer. It's connections (constant, switched, ground, and speakers) are all connected to the wires from the Honda harness.

I recently discovered that there is a bit of noise that belongs solely to the CD receiver. But it only becomes audible in AUX mode, with nothing playing, and the volume up way beyond the highest level I can stand.

My major concern is that since the time I have wired the empeg's constant (yellow) line to the battery, much more noise is noticeable with the empeg running. I still have to pause playback to hear it (I can also hear it during "quiet" parts of a song), but it becomes audible at a much lower volume level than the CD receiver's own tiny bit of noise. This noise, coming from the empeg, changes pitch both with the engine and with the empeg's drives spinning up. Also, the noise does not disappear or become quieter when the engine is off.

P.S. - You asked.