I'm not well versed on American Indians in the South, so someone else can jump in on that, but for a good general view on Southern history, you have to look at essentially two things that defined the South: slavery and the Confederacy/Civil War. I'd begin with American Slavery, American Freedom, by Edmund Morgan. Its older, but still good. It details the transition from white indentured servitude to African slavery in colonial Virginia. Then look at a solid overview of slavery in the Old South. Anything from David Brion Davis or Peter Kolchin's American Slavery are good bets. Next, look at Southern Honor, by Bertram Wyatt-Brown, another classic. See also The Confederacy as a Revolutionary Experience, by Emory Thomas, that details how the Confederacy began with certain goals and beliefs, and eventually abandoned (to some degree) those goals for the sake of independence. For post war stuff, see The Myth of the Lost Cause, Gary Gallagher, et al. It chronicles the Lost Cause myth following the war. Lastly, a great overall look at Southern history is Away Down South, by James C. Cobb.

Hope this helps! If you'd like more books on specific aspects like Jim Crow, the War, etc. I'd be happy to provide what I can, but I think these are good places to start. You can't understand the South today without understanding the South of 150 years ago, and you can't understand that without understanding slavery's existence and role in how dang near everything in the South functioned. You may run across some of the classic works from guys like Kenneth Stampp, Gene Genovese, or C. Vann Woodward, which are fine to read, BUT, there is better, more updated scholarship that may also be easier to read and understand.