In my small shop, I find myself doing things much in the same way as Brian. I have a box of necessary tools and small parts for each machine as near to the machine as possible. I also have a few shelves dedicated to normal wear parts, sanding rolls, discs, belts, blades, etc.
I've also familiarized myself to the point where I know every inch of all my machines and their own specific needs.
(I also always read the manual)