If the substrate is semi-infinite, then the metamaterial span can be set to 0 since the substrate is not considered to be part of the metamaterial. The metamaterial span setting is used to calculate the phase compensation for the phase accumulated in the background material between the source and monitors which is discussed on the parameter extraction page here:
The phase accumulation distances are illustrated here:
For example, the distance travelled in the background medium between the source and transmission monitor is the distance between the source and monitor minus the span of the metamaterial. Since the span of the metamaterial is very small compared to the wavelength of light even when using multiple layers of graphene, you can use a metamaterial span setting of 0.
For multiple layers of graphene, the “conductivity scaling” factor of the surface conductivity graphene material in the material database can be set to match the number of layers. This is discussed in the paragraph below figure 1 on this page: