Trim, elevaters, airlerons and so on. The FE was indeed responsible for the engines. I hope someone can chime in with the exact procedures.
I'm not sure of a B29, but my experience of 3 crew four engine heavy props are something like:-
FE controls start, and checks, under command from P1
Handling Pilot adjusts power during taxi.
FE checks mags, sets props, mixture, and cowl flaps, "E" handles if necessary etc.
Handling pilot sets take of power.
Engineer guards throttles, and trims take off power. Handling Pilot responsible for abort.
Climb, and cruise power set by Engineer at command of handling pilot.
Descent power reduced, and set by handling pilot.
Descent power trimmed by FE, and changes called by Handling Pilot to FE.
Approach, landing, and taxi power set by handling pilot.
NB:- Looks like enough room for a football match in there...! LOL