Who was the top commander of the confederate army?

Answer 1

There wasn't one until the last few weeks of the war, when Robert E. Lee was made General-in-Chief.

That role had been notionally filled by the Confederate president, Jefferson Davis, who felt his record as a Colonel in the Mexican war equipped him for high command. This was disproved almost from the start, and his feuds with the other Generals greatly slowed down the Southern war effort.