Additionally, in civilian aircraft requiring two pilots, the policy is each takes a leg of the flight, while the pilot not flying takes care of radios and other cockpit duties. The captain, regardless of who's flying, is still the pilot-in-command, responsible for the safe conduct of the flight.
Interestingly, my understanding is that on long trans-Pacific flights, where there's usually a relief pilot on board, the captain is still PIC, even though he or she napping in first class.