Pokies can certainly be a problem when you have different colors of thread, but it's possible that you are actually seeing the thread from the other side through the needle holes. These holes will probably close up when the quilt is washed. I would try making a small quilt sandwich with the same fabrics, thread, and batting. Quilt it and then spray it with water, rub your fingers over the holes, and see if you can still see pokies. If not, you may have the tension adjusted sufficiently to quilt with white on top and navy on bottom.