let me say first i am in no way an expert of car audio stuff, i just know what i know from experience. i have never powered speakers off an amp, so, while i do know it will help power the speakers better and give a better sound, i've found sometime it just takes a little tuning to get it all right. does your HU have built in crossovers? that may attribute to the bad sound. whenever i've powered a sub and amp the speaker sound has always been effected, just tweaking the crossovers has cleared up the distortion and made the speakers sound perfect. i have polks in the front doors, the mmc690 i think...anyways, they have built in tweeters and come with crossovers. i think these speakers are the best sounding speakers i've ever owned. i have alpines in the rear and they lacked the higher end sounds, so i added some tweeters and now everything sounds great! point is, i'm not running the speakers off an amp, i have heard my speakers powered by an amp (when i purchased them at tweeter i heard with and without), and the sound was better.
maybe start by singling out the speakers (using the balance and fader) and see if it's the fronts, or rears that don't sound good. and remember, you have stock tweeters in the dash too. i don't know much about your headunit, but read a little into it and see if there are some functions you didn't know about to tweak it better. I normally run 2 10" JL subs off a kenwood 600w mono-channel amp, but i haven't had it in for a few weeks because the system sounds great with and without them.