He will work with Democratic senators to set their agenda during his term, and part of that is decisions regarding whether to keep the filibuster or whether to push to end it, or to work around it. He can express his will via the bully pulpit, and via communication & coordination with Senate Dems, the same way basically any president has been able to convey their agenda to the senate for as long as we've had presidents and senators.
Obama and Harry Reid had this exact conversation over whether to continue using a filibuster, and Obama listed it in his autobiography as a regret that he didn't accept Reid's suggestion to nuke the filibuster.
