I have a Bernina 830E and when I machine embroider, I must hook the bobbin thread twice to get the proper tension. For regular sewing, I only hook once. And I always check to see that the bobbin thread is not showing when I first start stitching the project and make adjustments then. As for next time, I suggest you use a bobbin thread to match the sweatshirt or jean jacket or whatever.
When I first read your quest for help, my first inclination was to suggest your pigma pens. I had my 4Hers do this when their stitches showed. Old trick!