Captain reports to Fleet Captain who reports to Base Captain who reports to Fleet manager who reports to Flight Operations Director who reports to the Board. Or variations on that theme.
On the aeroplane, there is nobody senior to the Captain, though some would like to think so! But the Captain should still obey directions from the company or explain his reasons for not doing so, and at all times obey the directions in the Flight Crew Orders book, or have an extremely good reason not to! And operate in accordance with it at all times.