1. Did you loosen the top tension? You might also have to tighten the bottom tension (involves tightening screw on bobbin case; instructions online). For invisible on top and cotton in the bottom, the bottom tension has to be tight enough to pull the top thread down. If you do everything and still can't get the dots to go away, it's probably best to switch to a matching cotton thread in top and bottom.
3. You start in the middle *of an edge* and work to the other edge. You don't start in the dead center of the quilt.
4. A variegated thead can be nice.
Have you done SID before? I personally stopped doing it because it makes me too tense trying to stay exactly straight all the time. Now I use a walking foot and make wavy lines instead.