So this is a polarized capacitor? If so, then you cannot charge it with the Van de Graaff generator. The leakage resistance will be too great for the Van de Graaff. And even if it were not, the output voltage of the Van de Graaff would exceed the breakdown voltage of the capacitor. However, if you are trying to charge a lab type parallel plate capacitor, like http://en.wikipedia.org/wiki/File:Plattenkondensator_hg.jpg" [Broken] one, then the polarity does not matter.
Edit: Well, yes it does matter, sort of. The top of the Van de Graaff should connect to the "insulated from ground" plate of the parallel plate capacitor.