If you are using a 90/14 that is a big needle. Coats and Clark is not a very thick thread - unless you are using Quilting Thread - it wouldn't need that large of a needle. I would try a Quilting Needle in a smaller size. The other posts that mentioned your batting may also be on the money. If your batting is thin the stitches will never hide in it and high contrast wil definitely show through. If all else fails I guess try the Sharpie marker trick!