Columbia, South Carolina and Hickory, North Carolina seem to be the only major cities in the Deep South that Germans settled in any great numbers. My understanding is there were also minor settlements in New Orleans, New Braunfels, Texas, and Sarasota, Florida. Other than that, there were very little German settlements in the South. Why?
Why was the North more desirable to them than the South? Even today in the South, despite migration to the Sunbelt there is very little in the way of German influence and culture in the South.
I can't explain why later waves of German immigrants went primarily to the midwest, but you're dead wrong about there being very little German immigration to the South. The Carolina backcountry was settled largely by Scots-Irish and Germans (Pennsylvania Dutch) coming down from Pennsylvania. Not only Hickory (which is really not a major city, nor in the deep south), but a considerable swathe of western North Carolina and South Carolina was settled by mixed German, Scots-Irish, English, and others. The names of the old-stock residents (those who didn't anglicize them) reflect that fact, even if they've lost most of their connection with their ancestry and become generically American.
I hesitate to go much further, given that I'm not aware of any good academic resources on the topic, but if the mods will permit me a little leeway, I'll talk a bit more about my ancestral county, Gaston County, North Carolina. I'm drawing on Our Kin, by L.M. Hoffman, and The County of Gaston: Two Centuries of a North Carolina Region by Robert F. Cope and Manly Wade Wellman.
The first permanent white settlers arrived in the area which would become Gaston County (which lies two counties south of Hickory and Catawba County) in the late 1740s. These early families were almost entirely Germans: Hoyles, Hoffmans, Schmidts, Clemmers, Rhynes, Leinbergers. They were soon joined by other settlers of varied ancestry, but the Germans remained heavily concentrated in the northern part of the county. Full integration was a slow and halting process. The Lutheran churches continued conducting services in German until well into the 19th century, went bilingual for a generation or so, before switching to fully English services a little before the Civil War.