I have 3 machines. I have 3 different permanent sharpies, I have one color for each machines bobbin. All I do is color a little circle for which ever machine it goes with.

For multiple machines you could use this same technique but take a piece of masking tape and draw a circle in that machines bobbin color and tape the tape somewhere under the machine or on its lid so you'll 'remember' which color goes with that particular machine,