Using a higher loft batting can help with that, but at the end of the day, there is a reason why so many competition quilters use the exact same color & fiber for top and bobbin. Fidgeting with the tension can help, but it's not a guarantee and the more different the threads are the more likely you are to notice those pokies. They are present on every quilt, but when you use matching cotton threads, they will blend in the most. At least you used 2 poly threads, but I can't imagine any machine that would get them perfectly buried in a mid-low loft batting 100% of the time.