Desertion of Confederate troops often presented problems for occupying Yankee forces. "With Blood and Fire: Life Behind Enemy Lines" provides lots of details about Partisans, including deserters, who played hell with Union soldiers in Middle Tennessee. For the Confederate government, they were a mixed blessing because while the South badly needed more regular soldiers, the damage done to Union efforts and morale by these irregular troops was too great to quantify it. Some of the same was going on in Missouri, Arkansas, Kentucky, East TN and Virginia. This might be why Grant was so "generous" with the surrender terms he presented to General Lee at Appomattox.