In 1863, there was no "South Dakota." Dakota Territory, when it was organized in 1860, comprised what is now North and South Dakota, Wyoming, Montana, and small parts of Idaho and Nebraska.
Abbreviations:
Deu = Deuel
Brk = Brookings
Mnh = Minnehaha
Li = Lincoln
Col = Cole
Cly = Clay
Ya = Yankton
Jay = Jayne
Hut = Hutchinson
CM = Charles Mix
Brg = Bruguier
BH = Bon Homme
Ggy = Gregory
Tod = Todd
This map appears courtesy of the Gold Bug Historic Maps & Software.