there is a thread over at diymobileaudio.com about this-- titled something like 'help me build a computer to beat the bitone!!'
though i think that you might run into a couple of roadblocks running the headunit into the computer as a input, process the signal, and then out to the amps(i could be wrong though). my setup, and most of the others here also use the computer as the source-- so you play, and process the audio on the computer
if you can find it, there is a old wiki(they updated to a different version, but left the old info there) on processing audio through a computer, otherwise, just post up your questions-- either here, or in the high end sound area in the car audio forum here-- the car audio forum will get a little more attention than the newb area(esp. for audio processing), so just keep it in mind.
i have posted a lot on audio processing, so you could even just search for my username in the high end car audio section if you run stuck(there is also a car audio mod that keeps a link to the audio processing wiki in his sig, but i can't remember his s/n...).