I've had CX300's in the past, and I'm using my old ones atm because my Audio Technica's broke.
I think generally they are just very bassy and quite muffled out of the box. Coming from iPod buds, I'm not surprised that you're finding them very bassy, as the apple buds struggle to produce any deep bass that "hits" you.
It's a matter of letting you ears and perception of what sounds good adjust. When I went from CX300's (Bassy and muffled) to Audio Technica CK7's (Enphasized high frequencies) my ears would suffer from fatuige from the ammount of treble, but eventually I learned to like them, and not rate them as much better than CX300's.
About the EQ, I'm definately no expert, and am an amature like you, but the iPod EQ is fairly useless, and only distorts what you've already got, but if you want to reduce the ammount of bass, of make it sound like there's less, the bass reducer or treble booster will do this.
On itunes, when I select treble reducer on the EQ (which I can only assume is the same as the one on the iPod), the lower frequencies remain flat, with the higher frequencies become more pronounced. Bass reducer lowers the bass, but leaves the higher frequencies looking flat.
Hope this helps, I know I've rambled on a bit.
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