I love the look a variegated thread gived to a quilt so I use variegated all the time for the top or the bottom or for both. It depends upon what the quilt tells me would look best and the fabrics that have been used in the quilt. I have one that needs to be sandwiched and quilted that will not have variegated on the bottom, I think, unless DD asks for it because the bottom is a solid color. However, that doesn't stop me from using variegated thread either.
Chris