Brown v. Board of Education did not do either of these things. It had nothing to do with civil liberties or the separation of church and state. Instead, the case had to do with civil rights.
Brown was about segregation in public schools. It revolutionized the meaning of the 14th Amendment's equal protection clause. From the time that Plessy v. Ferguson was decided in 1896, the equal protection clause had been read to allow segregation so long as the separate accommodations for the races were equal to one another. In Brown, the Court rejected this idea. It stated that, with regard to public schools, segregation could never be consistent with equality.
This revolutionized the understanding of the equal protection clause. However, it did not do anything to impact civil liberties or the separation of church and state.