I understand Welles kept a diary covering much of is time in the Cabinet that is a wealth of candid information. It is published and available, last I heard. That is one on my 'wish list'.Both Navy Secretaries were very interesting and capable men.
Stephen R. Mallory was as well-prepared as any man I can think of to become Secretary of the Navy. He had served as chairman of the Senate Committee on Naval Affairs and had been involved in most of the naval reform efforts of the late antebellum era. His background was in the area of salvage and maritime law, and he knew many of the top officers of the Navy personally.
Gideon Welles was a newspaper editor and administrator whose sole contact with the Navy Department had been a stint in the Bureau of Provisions and Clothing during the Mexican War. He was intending to become Lincoln's Postmaster General; it is something of a historical curiosity that he was named Secretary of the Navy instead.
Both men proved to be very well-suited to their positions. Mallory, charged with creating a navy out of nothing (apart from a large number of naval officers who 'went South'), plunged into the immense task with great energy and skill. He had an uphill battle on every front-- scarce resources, influential personal enemies, and above all an opponent whose superiority he knew as well as any other man could. He was one of two of Jefferson Davis's Cabinet secretaries to serve the entire war in his position.
Welles, seemingly ill-prepared for his role, instead proved to be an effective and capable administrator; his lesser familiarity with naval affairs was quickly remedied by the appointment of former naval officer Gustavus Fox as chief clerk of the Navy Department, soon elevated to the newly-created post of Assistant Secretary of the Navy. The two made an excellent team, and Welles himself became one of Lincoln's inner circle of trusted advisors, alongside Secretary of State Seward (with whom Welles often tangled in the early years but became more accommodated to as time went on... in my view, as Seward learned his own position).