Just a short answer (maybe more at a separate time):
I keep my reference material totally separate from my task management material - different places, different structure, different everything. I do not even want them overly integrated. I want them for very different purposes, fundamentally. For sure there are synergies to be gained by firmer integration/coordination, but I usually get by with just links or similar directions to the reference material if I need it, but usually I have no problem finding what I need in my reference. It gets too complicated for me to even think about how to coordinate it all into one single structure.