Answer:
Lincoln felt it was important to also identify himself as commander in chief because as the president, he is also the head of the country's armed forces in not only foreign affairs but also internal affairs. He makes the decisions regarding war, and he can always be shot down using checks and balances, but as the president he makes decisions that he feels would be best for the country. In this case, what he feels is best for the country is that "the war will be prosecuted for the object of practically restoring the constitutional relation between the United States, and each of the States, and the people thereof, in which States that relation is, or may be, suspended or disturbed."