Usually when Luffy is absent from the crew, Zoro usually is the one in charge because he was the first to join thus he got the authority as the senior member of the crew. Of course if both Luffy and Zoro are absent then Sanji takes charge, vice verse. The only exception where Sanji took charge when Luffy and Zoro presents is when he advising the plan to take the keys from CP9 members in Enies Lobby which fulfilled his role as the advisor of the crew.