The separation of powers between the three branches of the federal is not a total separation. Each branch has control over the others to keep one from becoming more power than the remaining branches. This is known as a system of checks and balances. There is a second check in the division of power between the national and state governments known as federalism. When the Constitution was written, there was an attempt to create a national government with limited powers that allowed the states to retain most of their sovereign powers. Articles I, II, and III of the Constitution clearly delineate the division of power between the three branches of government in an attempt to keep any one branch from becoming more powerful than its counter parts. Article I clearly defines powers of Congress ‘to regulate commerce among the states and with foreign nations,” among others. I like the way Article II allows each state to take part in the selection of the President and Vice President yet clearly states Congress alone cannot elect them. Article III establishes the federal court system that oversees the court systems of the states. The Judicial branch, specifically the Supreme Court is the final arbiter and interpreter of Constitutional law. Article IV clearly establishes a set of checks and balances which apply to all states in the Union clearly outlining acceptable behaviors for all states. While the 10th Amendment states and I am paraphrasing, any power not specifically delegated in the Constitution is decided by the states.
The Founding Fathers understood local issues needed to be handled on the local level and Congress could handle issues with national implications. They were determined to form a Constitution which was inclusive of all states 'in order to form a more perfect Union.' By establishing a system of constitutionally mandated checks and balances, they were able to insure liberty and justice for all.