Even though I have a Bernina, which is supposed to be exceptionally good in terms of being able to adjust upper and lower tensions, I have found that it just doesn't work for me to use highly contrasting colors top and bottom when quilting, especially when free-motion quilting. One of the threads always makes some dots on the wrong side where it is pulled through a little.
It may have something to do with batting. It may be easier to use different colored top and bottom threads with polyester batting because it is thicker and fluffier, giving more leeway for a thread to be pulled slightly to top or bottom without showing. I prefer using fairly thin all-cotton or 80/20 battings.
Depending on the quilt, I have used invisible monofilament in the bobbin as well as on the top successfully. The secret to doing that is to be careful and not wind the bobbin too tightly. I wind mine slowly. Also, if your machine uses plastic bobbins, wind them only half full to avoid distorting the plastic. (There is still a lot of thread on the bobbin!). With my metal Bernina bobbins, I am careful to stop winding before any thread threatens to exceed the width of the bobbin as that can cause problems too. Finally, I loosen the top tension (again, because monofilament stretches).
If my backing fabric is light-colored and the top doesn't contain dark fabrics, I will often use a neutral thread in the bobbin and monofilament on top.
The problem I have always had is with a light colored bobbin thread showing on dark-colored top fabric, or dark-colored bobbin thread showing on light-colored top fabrics. The slight variations when free-motion quilting seem to disturb even a perfectly balanced stitch once in awhile, at least on my machine.