As far as i’m concerned, Organization should always be set up to allow anybody else in your facility to step in and find stuff in your box. I understand you may be a lone wolf, but if you use that rule, it will keep your project organized.
I always have a bin called FX, which is minimized and hidden from my view. I put all my motion effects in there. (much like your titles, i don’t usually need to access them, but i need a place to put them.)
Same for everything else. I create a bin called titles, audio in, and _sequences. (the _ keeps it at the top of my list)
I don’t use mixdowns at all. We go from offline to online in other boxes, and mixdowns are an easy way to kill that workflow.
For AAFs I always duplicate my timeline, put in a bin called “to sound”…and let it mess up that bin to its hearts content.
As you said at first, it has to make sense to you…for me, it has to make sense to everyone else as well, as we may have to jump on to someone else’s project at anytime.
Glenn