I tend to fill a little proud then scrape back to shape using a scraper or Stanley knife blade. This leaves a Matt or silk type finish. No end of techniques you can use. Brush the dried wax with a wire brush etc.Texture of wax fill is key to creating unobtrusive patches in my experience. If you melt the wax so that you have a large shiny flat surface, this attracts the eye more than hand-applied wax with an uneven surface. Try to match the texture of natural wood or knots if possible which can sometimes be done simply by softening the wax with hand heat and shoving it in the holes without melting or excessive smoothing.