My hubby made me a hanging cabinet with a glass door so that I can tell in a minute just what I have. I always put the bobbin right on top of the corresponding spool but have changed that idea.
Since I use all the same type of thread, I have a small box with the bobbins and just have to match the colors.
The bobbins didn't like sitting on top of the spools and if the cabinet jerked when opened, I was picking up bobbins from all over the place.
Have a separate box for the machine quilting bobbins......seems to work for me.