When using a Neutral Density filter with a Polarization filter is it best to put the ND on top or the Polar on top?

The best is to leave the ND in the bag and put a linear polar filter on top of the circular one. Now you have a variable density filter from about 2-3EV to total blackness. You need larger diameter linear polar filter (with an adapter ring) to avoid vignetting; they are cheaper than the circular ones.