This is quite similar to how I have things setup.
I have the following folder structure:
*Projects support materials
*Personal
*Archived
*Work
*Archived
Each OF project that is associated with a bunch of files has a folder here.
Sometimes, when I am a good boy, I create a link to the related folder so I can access it from within OF. More often though I manually just go in there because I know that its there. I find that in the heat of battle I don't have time to manage these links so I just rely on my system.
I think that you should really minimize all micro management as much as possible. And don't forget that you have spotlight at your disposal.
Of course if you are creating structure for others to understand it might be different.