I had wondered about this, too...I usually will end up matching the bobbin thread to the back, especially if dark backing...now, sometimes I have gotten small "pokeys", but in my opinion, I am not good enough with the fmq to have my back thread show up as bright as white thread would on black fabric...I also will just hand quilt, I like that anyway, and that way I can control my stitches...just boils down to what you like, and what you are comfortable with...good luck,
K