The attribution of his children between his wives is not certain. TSP(Atholl) does not even try to say which child was by which wife but BE1883 does give a lead. However, with TSP naming more daughters than BE1883, with some names being duplicated, some doubt remains on this matter which may be researched further in due course.
BE1883 (Stewart of Atholl) and TSP (Stewart of Atholl) differ in their records of John's children. We broadly follow BE1883.
Their only son John was created 1st Earl of Atholl in 1629. His son John (1st Marquess of Atholl)'s son John became 1st Duke of Atholl, ancestor of the present Dukes. The Earldom of Tullibardine was passed to William's brother Patrick.
After the death of her father (the 5th Earl), Mary's mother (Mary Ruthven) married John Stewart, 6th Lord Innermeath, who was created Earl of Atholl in 1596. This marriage between the younger Mary and James (2nd Earl of Atholl of the new creation) was therefore a marriage between cousins. James dsp in 1625 and the Earldom reverted to the Crown but was then granted to Mary's nephew John Murray (see above).