It's not you, it's iTunes. You are at the bleeding edge, with your multiple devices, etc., and iTunes is designed for the 99.99999% of people who just want to sync with their ipod.
You might want to consider experimenting with MediaMonkey (
http://www.mediamonkey.com ). It's free, and is kind of an "iTunes for power users." I'm not sure it'll do everything you want (and you'll still need iTunes for some tasks, like downloading podcasts from the iTunes store, which, last I looked, MediaMonkey couldn't do), but playlist/storage control is something that MediaMonkey is light years ahead of iTunes on.