You can select a drainage boundary for each layer if you select the time-dependent consolidation analysis option in Settle3D. If this checkbox is selected for the layer, then the layer is assumed to be freely drained at the bottom (i.e excess pore pressure will be automatically set to zero at the interface between layers). Otherwise, if this checkbox is not selected, then the interface will not be a drainage path (i.e. excess pore pressure can exist at the interface).
Use Soil Layers dialog to specify layer drainage conditions
In general, you can select “drained” at the bottom for the last layer of the model unless there are layers in the model that are sands, in which case you may need to consider drainage at the bottom of these layers.