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.