Actually I find iTunes to be a very straight forward piece of software. Before I used iTunes, I made sure all my music was encoded that iTunes can accept. Then, after syncing to my iPod, I straightened out the tagging that iTunes thought would be appropriate. After a few nights of straightening this out my music has never been more organized.
As far as bass boosts is concerned, yeah, the iPod truly sucks at this as well as the other EQ settings. Players such as the H300 series, iAudio X5 and D2 tramples the iPod's EQ to pieces. It's best to listen to the iPod with no EQ.