It has been the practicee of the incoming President since 911 to keep the existing DoD Secretary on for at least a year or so.

Secretary Carter has extensive experience with the Department of Defense. It would be wise for President Elect Trump to ask Secretary Carter to stay in place for at least the beginning of his first term.

The terrorist attacks on the USA was successful during those first years of President Clinton in 1993 and President Bush in 2001. The transition was more secure in 2009 with then Secretary Gates stayed with the Obama Administration until 2011.

That approach might be a good practice for Homeland Security and Mr. Jeh C. Johnson. With those two national security Secretaries in place, President-Elect Trump will have time to focus on the remaining offices of his cabinet. 

Washington, Nov. 14, 2016 — The ties between (click here) the Defense Department and commercial technology and innovation keep the U.S. military agile as it meets today’s challenges and remains ready for the future, Defense Secretary Ash Carter said today.
In a forum hosted here by The Atlantic magazine and innovation firm 1776, the secretary discussed DoD’s technology partnerships and the Force of the Future with The Atlantic’s editor-in-chief, Jeffrey Goldberg
While DoD focuses on five evolving threats from China, Russia, Iran, North Korea and the Islamic State of Iraq and the Levant, “I also need to make sure that we're ready for things that we cannot foresee today -- as ready as we can possibly be,” Carter said....