I also use pony tail stretching things and stack a couple of the same colored thread bobbins on my second thread spindle. That comes in handy when I take my machine to classes, knowing that I have prewound bobbins right on my machine.
Someone gave me a clear plastic bobbin case with a sponge bottom that has holes cut to hold bobbins. I love it, I can see the colored thread and the sponge keeps the threads from 'unspooling' themselves.
I only use Superior Bottom Line thread in my bobbins. I only use several colors that will match with any light, medium, or dark fabric and red. I don't buy colors to match all the fabrics or projects I am working on. Not necessary in my case.