I have an 05 40' FDQS and had a similar issue. If it is a FDQS the access to the engine compartment from inside is through a L shaped cover just as you step up on to the rear side of the bed. It is held in place by screws going into the wall below the closet and into the floor. Access to the engine compartment is limited form that area. I reinstalled my heat shield using strips of aluminum I purchased at Lowes and attached them to the underside of the floor with wood screws. As for the creaking sound the structure below the floor broke apart just before the little night stand on the back wall of mine. If you remove the drawer below the closet you should be able to get in there to repair it. I would not hesitate to take in for service with the heat shield laying on the valve cover IMHO. Mine was laying on the engine valve cover for sometime before I found it.
Wayne & Kathy
05 Alpine 40FDQS #75330 Towing 24' car hauler, 2012 Spyder, 2003 Harley FatBoy