So here's what I learned from this process:

All of my prior "by ear" adjustments to the EQ did not take into account the fact that there were definitely some sharp notches and peaks in the overall spectrum. I found some surprisingly narrow bands that needed correction.

In the past, with my "by ear" adjustments, a narrow peak in the midrange spectrum would sound irritating to my ear, so I would reduce the overall midrange of the system to get rid of the irritating peak. What I didn't realize until today was that I was killing all sorts of other perfectly good frequencies in the process of trying to correct that one tiny little peak.

In essence, I was making my stereo sound "less irritating" rather than "better".

Not only that, but the narrow bands that needed correction were NOT centered around the default empeg EQ frequency bands. I had to alter both the frequency and the Q of a few of the bands in the equalizer to nail the specific problems. Having the empeg's highly configurable equalizer made this SO much easier than it would have otherwise been.

The beauty of it was that I could place my mouse cursor on a specific peak in SpectraLAB, and it would give me a digital readout of the frequency. All I had to do was walk over to window, point my remote at the empeg through the window, and alter one of the EQ bands to be that exact frequency. Then mess with its level and Q until I flattened out the peak in the spectrum graph without over-affecting the neighboring bands.

I was unable to get it all perfectly flat, but that wasn't my goal. I just needed to correct major errors in the overall spectrum.

I also discovered that I had a severe hole around 100-150hz in the low end because I was overzealous with the crossover on my rear deck speakers. Correcting this by lowering the crossover and re-EQing that range made the bass sound much more natural and less boomy. I was pretty proud of how non-boomy my system sounded already, and this made it sound even better. The bass frequencies are now more natural overall, while still being loud and punchy.

Now there are whole areas of the mids and low-mids that are back in my music that weren't there before. Everything seems to have more presence and clarity. The stereo image seems better (taking into account the fact that my car's stereo image is pretty poor to begin with).

I haven't had a chance to live with it in the long term yet. I haven't even taken it on a drive to see how road noise enters into the equation, but so far, I like what I'm hearing.