FROM two tiny rooms high up and far back in St. Augustine's Episcopal Church, with its neo-Georgian archways, straight-backed pews and simple, graceful detail, the legacy of slavery in Manhattan looks down. The stone church, on Henry Street near Montgomery Street on the Lower East Side, was built for a patrician white congregation. But although it was completed in 1828, a year after slavery was legally abolished in New York State, behind the balcony and on either side of the organ are two cramped rooms, built so that black churchgoers could worship there without being seen by white parishioners.