I've been taught to pull the bottom thread up to the top of the quit before you start the stitching. This keeps knots from forming on the back of your quilt. This youtube shows what I'm trying to explain at about the 2 : 05 minute mark. I also like to hide each of the thread tails inside the quilt, instead of snipping them off. This gives a little more security to the end of your quilting lines.
Free Motion Quilting, Beginner Tutorial 3 (of 4) - YouTube