My opinion is: If you want the quilting to show texture only then use the color of the area on which you are quilting.
If you want it to show new design (the quilting) then use a contrasting thread. However, to do this you might need to find a color that will show equally on both colors. It also depends on your quilting design. If the quilting will show only in the specific sections then self color is good. If the design goes over the different colors then that is a different matter. This is basically what I as a quilt judge would look for. Let me know if this doesn't make sense or isn't clear.