Abraham Lincoln
Lincoln was not a general, and had only been in the army for a short time during the Black Hawk War.  However, he still took a major role in the war, often spending days and days in the War Department.  His plan was to cut off the South by surrounding it with ships, control the Mississippi River, and take Richmond, the Confederate capital.  He often clashed with generals in the field, especially George B. McClellan, and fired generals who lost battles or were not aggressive enough.  Eventually, he made Ulysses S. Grant the top general in the army.