Welcome from NC!
I use different colored threads on top and bottom alot. Sometimes you can get them balanced just right if the thread weights are identical, sometimes if the backing fabric and the quilt top are different weights you can do better with different weight threads (heavier on top and lighter weight on bottom if backing is a lighter weight fabric than top). I love the idea of using variegated thread to smooth out the oopsies (nice one Tartan!) and will be trying that one post haste.
Another thing to remember is that as the quilt fluffs up, whether from relaxing coming out of the quilting tension, or after it has been washed, much of the threadwork will sink into the topography, and not be very noticeable at all.
Post pics when you decide on a combination...curious minds want to know.
Alison