I just finished quilting a small quilt that had lots of thread changes. I don't think I'll do that one again. I used black in the bobbin, so didn't have to change that thread every time. I ended up spending about two hours burying thread tails.
Try gray for your quilting thread. It might just blend in perfectly.
Another option would be to use green in the upper and blue in the bobbin. You probably will have to make adjustments to the tension, but with fleece on the back, the top thread might just bury itself without much adjustment.
bkay