I frequently use a different color thread on the bobbin for quilting. I use fleece backings on my comfort quilts and match the thread to the backing fabric in the bobbin and match the thread to the top of the quilt for the top thread.
I do what I call utility quilting. Usually 1/4" outline stitching to secure the front to the fleece backing. I have very limited free motion skills, so blending my thread in is always my goal.
