When I start a project whether it is piecing or FMQ, I fill 2 or 3 bobbins ahead. I also have at least 1 bobbin dedicated to each color of thread that I have. The bobbins are attached to each spool using a Bobbin Mate and stored that way.
http://www.joann.com/bobbin-mate-18-pkg/7419534.html and I use Bobbin Wraps
http://www.anniescatalog.com/detail.html?prod_id=92274 to keep the bobbin thread from unwinding. I haven't been able to find them locally so I have ordered them on line. They are used for little girls ponytails.