The problem with the EQ settings on the iphone is that there are already pre-made (you can't adjust the specific range), so it's just like Electronic EQ, Jazz EQ etc... And worst of all, it doesn't apply to every app, it only applies to itunes/music app. So if you want to go on spotify or pandora on your iphone, it will have no effect. That's why I am planning on getting a nexus 4 (If i'm not broke from tons of different purchases by then).
In regards to the EQ what you've indicated is correct. If one has a desire to adjust a specific frequency, they have to do it in iTunes, then re-save the song so the EQ setting is embedded in the song - or, that's how I've understood it to work and have tried it a few times myself. The older iPod "Classic" at 30gb, was the one with the Wolfson DAC. The software also included a "Loudness" setting with the pre-set EQ. It was probably the only setting that I found useful at all.