I think that Jefferson's presidency was impacted by John Marshall's landmark decision in a couple of ways. The first was that Jefferson had to acquiesce to the fact that he could not simply assume that the Supreme Court would be an extension of the political party in power. Rather, he had to understand that the discussion of Constitutionality would rest in the hands of the Supreme Court.
In representing the essence of divided government and separation of powers, Jefferson's presidency was impacted by the idea that the Supreme Court remained distinct from the other two branches. In a way, this helped to feed Jefferson's Republican agenda of laissez- faire. This doctrine of government is one in which the role of the federal government is kept in limited reach.
Marbury v. Madison feeds this in the idea that the policy making branches of government cannot intrude upon the sanctity of the Supreme Court. Jefferson understood clearly the implications that this carried on his presidency. He would have to recognize the sovereign power of the Judicial Branch and not seek to dismiss it, as previous Presidents might have done. This reconfiguration of judicial power impacted his Presidency and each subsequent demonstration of executive order.