The main evidence that reveals this is the fact that Confederate generals typically won battles during this period when they were outnumbered by their Union opponents. A major example of this was what General "Stonewall" Jackson was able to do in the Shenandoah Valley in 1862.
There were also other instances of the Southern generals simply being more clever and inventive than those of the North. An example of this is the Second Battle of Bull Run. In that battle, Lee split his command and sent Jackson around Pope's troops instead of accepting a head-on fight. When Pope moved to fight Jackson, Lee used quick maneuvering to take up a position on Pope's flank and attack his army before Pope realized he was there.
A number of incidents such as this, where Union armies lost due to greater tactical skill on the part of the South, shows that Confederate generals were consistently doing better than their opponents.