When calculating volumes of reagents to add during cell separation (specifically positive-selection methods), should the cell number reflect the total cell count or the viable cell count?

Use the total cell count, because there will also be dead cells positive for your marker in question, often at the same frequency as the live cells. Since dead cells tend to bind non-specifically to antibodies and MicroBeads, they can reduce the amount of antibodies and MicroBeads available, and the staining of the live cells may be inefficient. Therefore, include both live and dead cells in your calculation. In samples with a low number of dead cells, however, this will not make a difference.