[BevvyB]

I can see by the way you're saying things like 'To Do Lists' that you may not be coming from GTD land

Step One: Read 'Getting Things Done'

Step Two: Tell us how you got on

(If you've already read it I apologize, but it seems from your post you may not have. You sound a bit overwhelmed with 'stuff' and if you were 'doing' GTD you probably wouldn't be)

Many people on these forums use Ominfocus for their 'doing' lists (or as we call them, next actions) and OmniOutliner for stuff as you say which is more project brainstorming notes than actual 'stuff I need to do'. Others use Evernote or other apps to manage their notes.

Omnifocus does do notes, but it's not designed for it. I've tried using OF for note taking as well as to do list making and it's not cut out for it. And the consensus around here tends to be that's not what it's really for, although you can use it a bit like that but it's a bit cumbersome.