I just ran into this but not with applique. My backing has a lot of white with tiny navy flowers, and the white quilting lines were nearly invisible. But I needed to do some stitching in navy and finally went with navy in the top and bobbin. It looks very nice on the back, like a secondary design. Of course, mistakes show up rather well that way, but the ones I can't easily fix will be part of its charm. I'd do that way before I put any ink on it.
Hugs,
Charlotte