The highlighting on Atom is pretty bad and hard to see when using find replace. Change it by 'Atom -> Styleshee' and adding:
atom-text-editor::shadow .highlight {
  &.find-result .region,
  &.current-result .region,
  &.current-result ~ .highlight.selection .region {
    z-index: -1;
  }

  &.find-result .region {
    background: yellow;
  }

  &.current-result .region,
  &.current-result ~ .highlight.selection .region {
    background: orange;
  }
}