According to the detailed biography of William C. Whittle, jr., included in the volume THE VOYAGE OF THE CSS SHENANDOAH: A MEMORABLE CRUISE, (see page 8-9) Whittle was never aboard the CSS ATLANTA. It indicates that by March, 1863, he was already on his way to Europe, where he remained for the rest of the war.
Where exactly did you see the reference that he had been on the CSS ATLANTA?