Yes marking the bobbins to the machine would be the best way I think. I have 2 machines, but the bobbins all look different. The Pfaff has plastic bobbins my one Bernina takes metal bobbins and my other Bernina takes the Big Bobbins. I do keep them in special areas with the machines and they each have their own containers. I like the donut holders that stop the thread from unwinding.