There is no restriction in MIKE SHE on the number of numerical layers in the SZ model. However, there may be practical limitations depending on your computer resources. As a rule of thumb, each additional SZ layer will significantly slow down your simulation.
The upper boundary of the top layer is always either the infiltration/exfiltration boundary, which in MIKE SHE is calculated by the unsaturated zone component or a specified fraction of the precipitation if the unsaturated zone component is excluded from the simulation.
The lower boundary of the bottom layer is always considered impermeable.
In MIKE SHE, the rest of the boundary conditions can be divided into two types: Internal and Outer. If the boundary is an outer boundary then it is defined on the boundary of the model domain. Internal boundaries, on the other hand, must be inside the model domain.
The UZ model only interacts and exchanges water with the top SZ layer. Therefore, the bottom of the top SZ layer is usually specified below the lowest water table level, so that the top SZ layer always includes the water table.