If you are not using an out of the box Lens, for example say Business Unit is your bottom entity, then you will likely need to update the script include, sn_ds.DSLensLeafEntityMapping, to add your bottom entity reference.   Also, you should make this configuration change before you do anything other configuration in Data Separation as you will end going in circles trying to sync things.

In the example below, we have our Data Separation Lens such that Business Unit is the bottom entity.  We added Business Unit [u_business_unit] to sn_align_core_planning_item and setup appropriate Lens integration as well.  We now change to Data Separation scope and open teh script include sn_ds.DSLensLeafEntityMapping.  Modify the LEAF_LENS_ENTITY_MAP and then save.  See example below in bold blue.