as you might have seen from other posts I had my empeg reinstalled (and I am having some issues with the driver's side speakers in my car.) However, when I had the factory stereo in my car, the sound actually sounded better than after I had my empeg installed. Is this normal? I saw the website about optimizing the sound on the empeg and I am going to try that...but it seems that there is a lot of midrange and not much treble. What do most people have their equalizer settings at?

If you're having trouble with your speaker outputs, correct those problems first. You might be experiencing trouble with your amplifier which could severely affect the sound quality. Don't worry about sound quality until after you've fixed whatever hardware problems you're having.

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it seems that there is a lot of midrange and not much treble.

That's probably just this issue. Your factory stereo came pre-tweaked. Or it could be that your MP3 encoder is rolling off high frequencies as described here.

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What do most people have their equalizer settings at?

Wrong question. Please read this.

I had that same problem in my Volvo. The stock radio/speakers had so much bass that I turned it down from midline. The empeg playing through those speakers didn't have the bass except when it hit those "sweet spots" in the low range. Must be tweaking.

It's not terrible, as I've been dealing with it for over 3 years (wow!). I can only hope a set of carefully selected speakers, AutoEQ, and Brad's instructions will make it sound better.