I have heard of batting bearding thru, but have not had that problem. I just quilted a large quilt with light, medium and dark purple with a natural muslin border. I used a soft green for the quilting. I have found it you match the thread to something, it will disappear as it hits the color you matched it to. Since then, I try to pick a color that contrasts, but does not stand out too much. Do you have some scraps of the top fabric you can audition the thread color on before committing to it? Don't forget, we want pictures!