During reentry, did anyone besides the Pilot manually control the orbiter?

No human ever controlled the space shuttle during entry. They tried it in the simulator and not one astronaut every survived the manual entry in the simulator. The ship completely flew itself. However, the pilot would take over at about 2500 feet (800 meters) and land it manually. They were quite capable of that.

The issue is the entry involves complex maneuvers using the RCS thrusters not aerodynamic controls. The computer was programmed to turn one wing into the air flow and then the other in order to manage heat. That would be quite complicated with a stick type control while maintaining about a 40 degree angle of attack. Once they got down to 50,000 feet (16 kilometers) the orbiter was down to about Mach 2 or 2.5 and aerosurfaces would work as expected. (There was also a concern about fuel dribble not evaporating and exploding on the next firing). The vehicle would stop using the thrusters and would instead maneuver using the aerosurfaces from that height down until the pilot took over manual control to land.