The skeleton could be what is holding up the ceiling of a vast cavern. That essentially, if you come in from the tail, gives you some side passages off of the body/cavern to "rooms" at the rear feet, a couple of larger rooms along the wings (perhaps several are just deadends), a couple more out to foreleg "rooms" then one at the head. You might even have the beast having died with its head near a forefoot/hand to make things a little less predicatable. Might be best to have the fossil/bones exposed in only a few areas, to give only early hints at where the PCs are exploring, then make things plain when they are in the skull.
I'd defintely make the fossil/bones lie in a 3D pose so that they are climbing upward into a mountain or down into the depths of the earth. The skull might look out from high in a mountain, for instance, and even be something that locals have dubbed as a promontory known as The Dragon's Skull, though they should be unaware of the actual relation to a fossil or bones.