Your filing system sounds perfectly fine to me. What's really important is not if it is "organized" according to an ideal, but if it's arranged in a manner that works and is intuitive for you.
I think you'll probably find as you become more and more used to the brain's capabilities, you will start adjusting things, and they will fall into cleaner organization patterns. At least this is how it worked for me. I'm not sure if it's because my comfort level rose with the brain as I trusted it more, or if my thinking got clearer when the relationships are actually in front of you. In a similar fashion to Nick, I have jumps of my home thought, Inbox, Waiting for someone, and Later. Inbox is everything I'm working on, and the actual items usually have two or more parents. Inbox and the area they belong in. Wating for someone usually has the item, another subject parent, and a jump to the person whose input I'm waiting for. This works fine for me, although I don't have everything grouped under a Life todo list. This seems like a pretty good idea also, sort of a macro overview. I'd highly recommend using thought icons, as it provides a quick visual cue of what area of thought it is. For example, my projects have the construction hat icon. Inbox has a folder Icon. People have a person icon. Good luck!
Java SE 6