I don't. I use those rubberized rings to hold the bobbins. They aren't with the thread. Each machine has its own ring labeled. And then there are rings for different thread types: aurifil vs. whatever else I use. I've never had a problem this way.
One friend taught me to use my extra spool pin pointing up to hold my bobbins for any one project as I like to wind multiple bobbins at once for my works.