Вам необходимо использовать AssociateRequest:
public void AssociateEntities(IOrganizationService service, List<Entity> secondaryEntities, Entity primaryEntity, string relationshipName)
{
AssociateRequest request = new AssociateRequest
{
Relationship = new Relationship(relationshipName),
Target = primaryEntity.ToEntityReference(),
RelatedEntities = new EntityReferenceCollection(secondaryEntities.Select(x => x.ToEntityReference()))
};
OrganizationResponse response = service.Execute(request);
}