I know there are gadgets out there for linking a spool of thread to its matching bobbin, but they don't seem to work well for me: putting things back where they belong is not one of my consistent strong points. I have started labeling my bobbins with those notebook paper reinforcements - the little doughnut-shaped stickons that you probably already have in a desk drawer somewhere.
I write the thread brand/type and the color code on the reinforcement in little bitty printing (hint: do this before you put it on the bobbin) and position it so the hole lines up with the one on the bobbin. Now I can identify which fiber and color is on each bobbin: no more Dark Navy Metrosene on top of the machine and Black Silk-finish cotton in the bobbin.
I would recommend checking the "fit" first to make sure that the reinforcement won't be peeled off by moving parts on your machine; a convenient label is not worth gumming up or jamming your sewing machine.