Both Presidents Lincoln and Davis faced many challenges during their time in office.
One of President Lincoln’s biggest problems was finding competent commanders. When the south began to secede almost 1/3 of all army officers resigned their posts to fight for the Confederacy. Many of these officers were superior to their Union counterparts, a situation that led to many defeats in 1861 and 1862.
Lincoln also had to contend with the possibility of foreign support for the south. Britain and France had sent supplies to the south on several occasions and the Confederate government was in active dialogue for most of the war with both nations. If he wasn’t careful, Lincoln might have had to deal with Europeans sending ships and troops south.
Davis had his own problems. One of his biggest obstacles was the lack of hard currency in the south. Throughout the war the value of Confederate money fell and issues surrounding inflation grew worse and worse. Since 95% of the nations gold specie was in the north, Davis had no real money backing up his paper currency.
Davis also had to deal with a country where the chief executive was weak. He was subservient to the states in many ways and lacked the necessary war powers a president needs to confront a national crisis.
The Confederates were also desperately short of almost all war supplies, especially near the end of the war, due to their lack of industrial capacity.