Single layer capacitors and die cavities

I am working on a design with single layer capacitors, bare die and cavities for the die. In the past we handled the die and cavity as an regular component. This is pretty simple and works well. The problem I'm having is with the single layer capacitors. We woudl normally create the casp the same way you would a screw or other piece of hardware, meaning it would get added to the BOM but not the .brd file. We really want a way to add it to the board file so we have reference designators and an XY location. I can create a single pin part and attach that pin to the net that the bottom surface of the cap is attached to, which is usually ground, but that doesn't associate the cap with the die in any way.