should I use high voltage or high current to burn carbon rods to dust
I would have to guess that with carbon having a very high melting point (evaporating point) that a high current (there-by high heat) DC voltage would be the best bet.  

In a vacuum you should not need too high a voltage to create a current, though you may need a bit higher voltage in the beginning to initiate the spark.

Using an AC voltage may not be good, as this would likely start to erode both of the carbon rods, (assuming this is unwanted).

Using some type of current level sensing to advance the +ve rod could be used, not at a 0 current point, but as the current level decreases below the value that works best.  Again I would assume that trying to maintain a constant current would give a more consistent coverage to a sample in the chamber.  The optimum current level would need to be determined experimentally.  (For example a servo like motor driving a worm gear as a linear positioning assembly. The direction and speed of the motor would be related to the amount of increasing or decreasing current.)

Placing the sample at a + DC bias may increase the coating effect by attracting ions of the carbon.