I use mine up that way too, so I have empty bobbins when I need them. I just use them, and don't worry about if one is cotton or the other polyester unless it is a new project that demands one or the other. The seams in the back of the quilt will hold together anyway. Look at those made 50 to100 years ago, they didn't have polyester anything in those days and the quilts are still alive and well.
One thing I found out thought, don't let a spool of thread sit on the thread holder above the bobbin winder, I found it wound around inside the machine on something and lots of it, all different colors, had to cut it off that rod with a fine scissors. No more thread on top of the machine besides the one I am using, I learned my lesson and now have a bobbin winder on the side.
Carol J.
CarolJ.