The Confederacy had internal railroads that they could have utilized to an advantage early in the war. The only time the South used them was at Chicamauga when Longstreet's Corps was sent from Virginia to Georgia. The Confederates had a tactical advantage that was not used. They could have used the railroads to move troops and overwhelm the Federal sluggish armies and obtained their objective.
The problem that plagued the Confederate railroads during the War was:
1) There never was a centralized, coordinated operation like the United States Military Railroad was.
2) The southern railroads had varying railroad gauges, and that proved to be a BIG problem moving anything throughout the Confederate states. I believe that the US Military Railroad used standard gauge (4' 8.5") for all their lines.