If you don't spring for a 4 channel amp you can increase the low-pass filter on the sub amp to restrict your sub to lower tones and perhaps use a crossover (software/hardware) to keep your speakers to the highs. I think this is how finch does it and the lyrics come across the bass really clean even when the bass is cranked. Also, I have a ported box for my two 12" Alpine subs and although it allows for very LOUD bass, I much prefer the cleaner hits that come with a sealed box. It's on my list of things to do before winter.
P.S.- I haven't spent a lot of time in cars with mismatched front and rear speakers, but I have spent a lot of time with a home theatre system that had a mismatched center channel. *shudders*

The stereo sound always sounded like it was taking a big deuce all over the vocal track.