Generally whichever object is created last will take priority and its refractive index will be used in the case of an overlap.
In your case if I understand correctly, I would actually only create air holes for the PBG crystal and use a large slab of material as the AG film covering the entire crystal structure.
As an aside, if you ever are not completely sure which refractive index the simulator will use (as in the case of an overlap) use the 2D and 3D Refractive index viewers, which you can find at the bottom of the Layout window. It will allow you to look at 2D slices of the simulation domain and view the refractive index.
Regards