I have a bunch of bobbins with all different colors on them. I use them all. I do not use the black threaded ones on something that I am working on that is white. But for everything else...use them all.
Recently I filled 6 bobbins with this cream colored thread. They would not work in my machine to save my life. I go to my sewing class and the bobbin is still in the machine and I tried sewing and nope don't want to work so one of the ladies came over and told me that I had Quilting Thread in it and not regular thread and that is why it wouldnt work. LOL But I use whatever color bobbin thread I have at the time.