What is the difference between the free exercise clause and the establishment clause?

The Free Exercise clause states that Congress cannot restrict your choice of religion, nor your exercising that religion. It must be an bona fide religion, however. You can't make up a religion for the sole purpose of bypassing laws. The Establishment clause means that the government will not set up a new religion, or endorse one over any other. This does not mean that you cannot belong to any religion to be part of government. It means that the government will not (suppose to) pass laws that benefit one religion over any other.