How did the founders define the judicial branch? Was any provision of judicial branch changed, when and why?
Alexander Hamilton once considered the Judicial Branch the most meaningless branch of government. From that particular point, the court has undergone some significant change. For example, the Judiciary Act of 1789, which to some extent limited the power of the court, was overturned by the landmark case of Marbury v. Madison, where Justice John Marshall defined the court's powers to include the ability to determine the Constitutionality of Congressional laws and Presidential actions. The Judiciary Act called for 6 justices, a number which later increased to nine. The overall purpose of the court ended up changing from its original conception as it became seen as the fundamental guardian and protectorate of the Constitution and its intent.
The founders really did very little to define the judicial branch of government. They said there would be a supreme court and some other courts (not specified how many). They did not say how many people would be on the Supreme Court. They said what kinds of cases the Court could hear, but the did not (and this is important) give it the power to say that laws made by Congress or by the states were unconstitutional.
The powers of the judicial branch were not changed by amending the Constitution. Instead, the Supreme Court took for itself the power to declare laws unconstitutional. This was done in the 1803 case Marbury v. Madison.