There are many institutions that have manuscript material related to Flannery O'Connor. This page lists many of these collections, but there may be others that exist or will become available in the future. Here are some quick tips for finding them.
Betty Hester, known as 'A' in the Habit of Being, was a long time companion of Flannery O'Connor. Hester's collection of personal papers and letters from O'Connor is owned by Emory University and is now open for research.
Series 1 Box 1 Folder 47 contains correspondence between Frank Daniel and Flannery O'Connor. The Frank Daniel Papers are located at the Hargrett Rare Book and Manuscript Library at the University of Georgia.
The Sally Fitzgerald Papers contain letters, manuscripts, and other records related to Flannery O'Connor located at Emory University. Fitzgerald wrote and edited many works about O'Connor, including the Habit of Being.