Organization to assist uprooted southerners after the civil war?

Freedmen's Bureau

One agency that helped former slaves was called the American Missionary Association and was a part of the Congregational Church (now a part of the United Church of Christ). The AMA founded colleges (among other things) to educate freed slaves. Six of those colleges are:

Fisk University, Talledega College, Tougaloo College, Huston-Tillotson University, LeMoyne-Owen College, and Dillard University.