Populated Multi List from Custom Entity

I have a request to create a custom entity (a list basically) that will be added and modified by Power Users.  This list will have a lookup to the Subject entity (1:N Relationship - One Subject to Many Custom Entity entries).

When a Case is created and the subject is chosen then on save a multi list is populated from that custom entity based upon the relationship from the subject lookup.

Does that make sense? The problem I am having at this time is figuring out how to reference that relationship from the lookup.  How does a lookup save it's relationship? I was looking for the SubjectID to reference on a queryexpression.