When stacking filters, the main principles are to a) minimise the risk of light leak b) achieve a balanced exposure in a single frame for long exposures.
My most common combination of stacking would be to place an ND filter with a GND filter. It is important to place the ND filter in the slot closest to the lens making sure that the foam gasket fits smugly against the filter holder itself. This prevents light leak more effectively than if the ND filter was placed in the outer slots. Save the outer slot for your GND filter and select the most appropriate strength and gradation of GND filter for the scene (eg. Hard vs Medium vs Soft). In the rare scenario that you need to stack two ND filters in order to achieve a long exposure during bright conditions, make sure that the densest ND filter occupies the first slot as these filters tend to be the most prone to introducing reflections through light leak.
NiSi V6 100mm Filter Holder Kit Review by Daniel K Cheong
by Dylan Toh