The Free Exercise Clause main purpose is to protect the right to any citizen to practice their religious beliefs, so it is the duty of the government to protect the freedom of religion.
The Establishment Clause main purpose is to limit the government from making laws that establish any official religion of the US or laws that are based on religious beliefs.
This means that all American citizens have the right to practice the religion they want, the government has the duty to protect this freedom but at the same time, the government has the duty to remain neutral in matters of religion.